Dikarya Dikarya is a subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota, both of which in general produce dikaryons, may be filamentous or unicellular, but are always without flagella. The Dikarya are most of the so called "higher fungi", but also include many anamorphic species that would have been classified as moulds in (inc. Deuteromycota The Fungi imperfecti or imperfect fungi, also known as Deuteromycota are fungi which do not fit into the commonly established taxonomic classifications of fungi that are based on biological species concepts or morphological characteristics of sexual structures because their sexual form of reproduction has never been observed; hence the name ")

Ascomycota The Ascomycota are a Division/Phylum of the kingdom Fungi, and subkingdom Dikarya. Its members are commonly known as the Sac Fungi. They are the largest phylum of Fungi, with over 64,000 species. The defining feature of this fungal group is the "ascus" (from Greek: ἀσκός , meaning "sac" or "wineskin"), a

Pezizomycotina Pezizomycotina contains the filamentous ascomycetes and is a subphylum of the Ascomycota . It is more or less synonymous with the older taxon Euascomycota . These fungi reproduce by fission rather than budding and this subdivision includes almost all the ascus fungi which have fruiting bodies visible to the naked eye (exception: genus Neolecta

Saccharomycotina Saccharomycotina is a subphylum of the phylum Ascomycota , and consists of yeasts - they form no ascocarps (fruiting bodies), their asci are naked, and they can reproduce asexually by budding

Taphrinomycotina Taphrinomycotina is one of three subphyla constituting the Ascomycota and is more or less synonymous with the slightly older invalid name Archiascomycetes (sometimes spelled Archaeascomycetes). Recent molecular studies suggest that the group is monophyletic and basal to the rest of the Ascomycota

Basidiomycota Basidiomycota is one of two large phyla that, together with the Ascomycota, comprise the subkingdom Dikarya (often referred to as the "higher fungi") within the Kingdom Fungi. More specifically the Basidiomycota include mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars,

Agaricomycotina The subphylum Agaricomycotina, also known as the hymenomycetes, is one of three taxa of the fungal division Basidiomycota . The Agaricomycotina contain some 20,000 species, and about 98% of these are in the class Agaricomycetes: most of the fungi known as mushrooms, including the bracket fungi and puffballs. Species in the Agaricomycotina that are

Pucciniomycotina

Ustilaginomycotina Ustilaginomycotina refers to a subphylum within the phylum Basidiomycota of the kingdom Fungi, consisting of the classes Entorrhizomycetes, Ustilaginomycetes, Exobasidiomycetes and the order Malassezia

Subphyla Incertae sedis Incertae sedis , abbreviated "inc. sed.", is a term used to define a taxonomic group where its broader relationships are unknown or undefined

Entomophthoromycotina

Kickxellomycotina Kickxellomycotina is a fungus grouping. The name was changed from "Harpellomycotina", because "Kickxellomycotina" had an older stem

Mucoromycotina Mucoromycotina is subphylum of Fungi of uncertain affinities. It contains 3 orders, 61 genera, and 325 species

Zoopagomycotina

A fungus (pronounced /ˈfʌŋɡəs/) is a member of a large group of eukaryotic A eukaryote is an organism whose cells contain complex structures enclosed within membranes. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. The presence of a nucleus gives eukaryotes their name, which comes from the organisms that includes microorganisms such as yeasts Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with the 1,500 species currently described estimated to be only 1% of all yeast species. Most reproduce asexually by budding, although a few do so by binary fission. Yeasts are unicellular, although some species with yeast forms may become multicellular through the formation of and molds Molds are fungi that grow in the form of multicellular filaments, called hyphae. In contrast, microscopic fungi that grow as single cells are called yeasts. A connected network of these tubular branching hyphae has multiple, genetically identical nuclei and is considered a single organism, referred to as a colony or in more technical terms a, as well as the more familiar mushrooms A mushroom is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source. The standard for the name "mushroom" is the cultivated white button mushroom, Agaricus bisporus, hence the word mushroom is most often applied to those fungi that have a stem (stipe), a cap (pileus), and gills. The Fungi (pronounced /ˈfʌndʒaɪ/ or /ˈfʌŋɡaɪ/) are classified as a kingdom In biology, kingdom or regnum is a taxonomic rank, which is either the highest rank or in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups called phyla or divisions in botany. The complete sequence of ranks is life, domain, kingdom, phylum, class, order, family, genus, and species that is separate from plants Plants are living organisms belonging to the kingdom Plantae. They include familiar organisms such as trees, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The scientific study of plants, known as botany, has identified about 350,000 extant species of plants, defined as seed plants, bryophytes, ferns and fern allies. As of 2004,, animals Animals are a major group of mostly multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and independently. All animals are also and bacteria The bacteria ( [bækˈtɪəriə] ; singular: bacterium)[α] are a large group of single-celled, prokaryote microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste,. One major difference is that fungal cells have cell walls A cell wall is a tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, and also acts as a filtering mechanism. A major function of the cell wall is to act as a pressure vessel, preventing over-expansion that contain chitin Chitin n (pronounced /ˈkaɪtɨn/) is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. It is the main component of the cell walls of fungi, the exoskeletons of arthropods such as crustaceans (e.g. crabs, lobsters and shrimps) and insects, the radulas of mollusks and, unlike the cell walls of plants, which contain cellulose Cellulose is an organic compound with the formula n, a polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4) linked D-glucose units. 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 In evolutionary biology, a group of organisms have common descent if they have a common ancestor. All living organisms on Earth are descended from a common ancestor or ancestral gene pool (a monophyletic In common cladistic usage, monophyletic describes a group of organisms that form a clade, consisting of a last common ancestor and all of its descendants. The term is not synonymous with the less common term holophyly, which does not include a last common ancestor. It is contrasted with the terms paraphyly, which is a taxonomic group consisting of group). This fungal group is distinct from the structurally similar slime molds Slime mold is a broad term describing fungus-like organisms that use spores to reproduce. Slime molds were formerly classified as fungi, but are no longer considered part of this kingdom (myxomycetes) and water molds Oömycota or oömycetes (pronounced /ˌoʊ əˈmaɪ sit is/), also known as water molds (or water moulds: see spelling differences), form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms. They are filamentous microscopic, absorptive organisms that reproduce both sexually and asexually. Oomycetes occupy both saprophytic and (oomycetes). The discipline of biology Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy devoted to the study of fungi is known as mycology Mycology is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicinals (e.g., penicillin), food (e.g., beer, wine, cheese, edible mushrooms) and entheogens, as well as their dangers, such as poisoning or infection, which is often regarded as a branch of botany Botany, plant science, phytology, or plant biology is a branch of biology that involves the scientific study of plant life. Botany covers a wide range of scientific disciplines concerned with the study of plants, algae and fungi, including structure, growth, reproduction, metabolism, development, diseases, chemical properties, and evolutionary, 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 In ecology, crypsis is the ability of an organism to avoid observation or detection by other organisms. A form of antipredator adaptation, methods range from camouflage, nocturnality, subterranean lifestyle, transparency, or mimicry. The word can also be used in the context of eggs and pheromone production lifestyles in soil, on dead matter, and as symbionts The term symbiosis commonly describes close and often long-term interactions between different biological species. The term was first used in 1879 by the German mycologist Heinrich Anton de Bary, who defined it as "the living together of unlike organisms." The definition of symbiosis is in flux, and the term has been applied to a wide of plants, animals, or other fungi. They may become noticeable when fruiting In fungi, the sporocarp is a multicellular structure on which spore-producing structures, such as basidia or asci, are born. The fruiting body is part of the sexual phase of a fungal life cycle, with the rest of the life cycle being characterized by vegetative mycelial growth and asexual spore production, either as mushrooms or molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling In ecology and Earth science, a biogeochemical cycle or nutrient cycle is a pathway by which a chemical element or molecule moves through both biotic and abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. In effect, the element is recycled, although in some cycles there may be places (called reservoirs) where the element is and exchange. They have long been used as a direct source of food, such as mushrooms and truffles A truffle is a fungal fruiting body that develops underground and relies on mycophagy for spore dispersal. Almost all truffles are ectomycorrhizal and are therefore usually found in close association with trees, as a leavening Bread is a staple food prepared by cooking a dough of flour and water and possibly more ingredients. Doughs are usually baked, but in some cuisines breads are steamed, fried, or baked on an unoiled skillet. It may be leavened or unleavened. Salt, fat and leavening agents such as yeast and baking soda are common ingredients, though bread may agent for bread, and in fermentation Fermentation in food processing typically is the conversion of carbohydrates to alcohols and carbon dioxide or organic acids using yeasts, bacteria, or a combination thereof, under anaerobic conditions. A more restricted definition of fermentation is the chemical conversion of sugars into ethanol. The science of fermentation is known as zymology of various food products, such as wine Wine is an alcoholic beverage, typically made of fermented grape juice. The natural chemical balance of grapes is such that they can ferment without the addition of sugars, acids, enzymes or other nutrients. Wine is produced by fermenting crushed grapes using various types of yeast. Yeast consumes the sugars found in the grapes and converts them, beer Beer is the world's most widely consumed and probably oldest alcoholic beverage, and the third most popular drink overall after water and tea. It is produced by the brewing and fermentation of starches, mainly derived from cereal grains—most commonly malted barley, although wheat, maize , and rice are widely used. Most beer is flavored with hops,, and soy sauce Soy sauce is a condiment produced by fermenting soybeans with Aspergillus oryzae and Aspergillus soyae molds, along with roasted grain, water, and salt. It is a traditional ingredient in East and Southeast Asian cuisines, and in more recent times is used in Western cuisine and prepared foods. Since the 1940s, fungi have been used for the production of antibiotics In common usage, an antibiotic is a substance or compound that kills bacteria or inhibits their growth. Antibiotics belong to the broader group of antimicrobial compounds, used to treat infections caused by microorganisms, including fungi and protozoa, and, more recently, various enzymes Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their produced by fungi are used industrially Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their and in detergents A protease breaks down proteins. A protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein. Proteases work best in acidic conditions except alkaline proteases. Its optimal activity is shown in alkaline(basic). Fungi are also used as biological agents A biological agent is a bacterium, virus, prion, fungus, or biological toxin that can be used in bioterrorism or biological warfare. More than 1200 different kinds of biological agents have been described and studied to date. Applying a slightly broader definition, some eukaryotes and their associated toxins can be considered as biological agents to control weeds and pests. Many species produce bioactive Pharmacological or biological activity is an expression describing the beneficial or adverse effects of a drug on living matter. When the drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other constituents. The main kind of biological activity is a compounds called mycotoxins A mycotoxin (from Greek μύκης "fungus" and Latin (toxicum) "poison") is a toxic secondary metabolite produced by an organism of the fungus kingdom, including mushrooms, molds, and yeasts. The term 'mycotoxin' is usually reserved for the toxic chemical products produced by fungi that readily colonize crops. Most fungi are, such as alkaloids Alkaloids are a group of naturally occurring chemical compounds which mostly contain basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. Beside carbon, hydrogen and nitrogen, molecules of alkaloids may and polyketides Polyketides are secondary metabolites from bacteria, fungi, plants, and animals. Polyketides are usually biosynthesized through the decarboxylative condensation of malonyl-CoA derived extender units in a similar process to fatty acid synthesis . The polyketide chains produced by a minimal polyketide synthase are often further derivitized and, that are toxic to animals including humans. The fruiting structures of a few species contain psychotropic A psychoactive drug, psychopharmaceutical or psychotropic is a chemical substance that crosses the blood-brain barrier and acts primarily upon the central nervous system where it alters brain function, resulting in changes in perception, mood, consciousness, cognition, and behavior. These drugs may be used recreationally, to purposefully alter one' 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. 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.

Contents 1 Etymology 2 Characteristics 3 Diversity 4 Morphology 4.1 Microscopic structures 4.2 Macroscopic structures 5 Growth and physiology 6 Reproduction 6.1 Asexual reproduction 6.2 Sexual reproduction 6.3 Spore dispersal 6.4 Other sexual processes 7 Evolution 8 Taxonomy 8.1 Taxonomic groups 8.2 Fungus-like organisms 9 Ecology 9.1 Symbiosis 9.1.1 With plants 9.1.2 With algae and cyanobacteria 9.1.3 With insects 9.1.4 As pathogens and parasites 10 Human use 10.1 Drugs 10.2 Cultured foods 10.3 Medicinal use 10.4 Edible and poisonous species 10.5 Pest control 10.6 Bioremediation 10.7 Model organisms 10.8 Others 11 Mycotoxins 12 Mycology 12.1 History 13 See also 14 Footnotes 15 References 16 External links

Etymology

The English word fungus is directly adopted from the Latin fungus (mushroom), used in the writings of Horace and Pliny.^[3] This in turn is derived from the Greek word sphongos/σφογγος ("sponge"), which refers to the macroscopic structures and morphology of mushrooms and molds; the root is also used in other languages, such as the German Schwamm ("sponge"), Schimmel ("mold"), and the French champignon and the Spanish champiñon (which both mean "mushroom").^[4] The use of the word mycology, which is derived from the Greek mykes/μύκης (mushroom) and logos/λόγος (discourse),^[5] 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.^[4]

Characteristics

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.^[6][7] 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.^[8] 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^[9]).
• With animals: Fungi lack chloroplasts and are heterotrophic organisms, requiring preformed organic compounds as energy sources.^[10]
• With plants: Fungi possess a cell wall^[11] and vacuoles.^[12] 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.^[13]
• 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.^[14][15]
• 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.^[16] Both fungi and oomycetes grow as filamentous hyphal cells.^[17] In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells.^[9]
• In common with some plant and animal species, more than 60 fungal species display the phenomenon of bioluminescence.^[18]

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.^[19]
• 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,^[20][21] 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.^[22]

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,^[23] 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.^[24] However, plants have an additional terpene pathway in their chloroplasts, a structure fungi do not possess.^[25] Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants.^[24] 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.^[24][26]

Diversity

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^[27] or ionizing radiation,^[28] as well as in deep sea sediments.^[29] Some can survive the intense UV and cosmic radiation encountered during space travel.^[30] 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.^[31] Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.^[32]

Around 100,000 species of fungi have been formally described by taxonomists,^[33] but the global biodiversity of the fungus kingdom is not fully understood.^[34] 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.^[35] 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.^[36] 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.^[37]

Morphology

Microscopic structures

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.^[38] The combination of apical growth and branching/forking leads to the development of a mycelium, an interconnected network of hyphae.^[19] 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.^[39] 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.^[40] Coenocytic hyphae are essentially multinucleate supercells.^[41]

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.^[42]

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.^[43] 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.^[44]

Macroscopic structures

Armillaria ostoyae

Fungal mycelia can become visible to the naked eye, for example, on various surfaces and substrates, such as damp walls and on spoilt food, where they are commonly called mold. 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.^[45] Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of a clonal colony of Armillaria ostoyae, which extends over an area of more than 900 ha, with an estimated age of nearly 9,000 years.^[46]

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.^[47] The fruiting bodies of the basidiomycetes and some ascomycetes can sometimes grow very large, and many are well-known as mushrooms.

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.^[48] Hyphae are specifically adapted for growth on solid surfaces, and to invade substrates and tissues.^[49] They can exert large penetrative mechanical forces; for example, the plant pathogen Magnaporthe grisea forms a structure called an appressorium which evolved to puncture plant tissues.^[50] The pressure generated by the appressorium, directed against the plant epidermis, can exceed 8 megapascals (1,200 psi).^[50] The filamentous fungus Paecilomyces lilacinus uses a similar structure to penetrate the eggs of nematodes.^[51]

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

The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol.^[52] 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.^[53][54][55] 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.^[56] 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,^[57] or growth by volume expansion during the development of mushroom stipes and other large organs.^[58] Growth of fungi as multicellular structures consisting of somatic and reproductive cells—a feature independently evolved in animals and plants^[59]—has several functions, including the development of fruiting bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication.^[60]

Traditionally, the fungi are 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.^[61][62] 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 only been described for a few species, the effects on growth rates are small, and the underlying biophysical and biochemical processes are not known.^[28] 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.^[63]

Reproduction

Polyporus squamosus

Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this kingdom of organisms.^[64] It is estimated that a third of all fungi reproduce by different modes of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph and the anamorph.^[65] 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 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.^[66] The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species which lack an observable sexual cycle.^[67]

Sexual reproduction

Sexual reproduction with meiosis exists in all fungal phyla (with the exception of the Glomeromycota).^[68] 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.^[69][70] Mating experiments between fungal isolates may identify species on the basis of biological species concepts.^[70] 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.^[71]

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).^[72]

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.^[73]

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.^[74] A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.^[75] 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.^[76]

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 travelling 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.^[77] 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.^[78] 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;^[79] 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.^[80] 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.^[81] Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.^[82]

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 parasexual processes, initiated by anastomosis between hyphae and plasmogamy of fungal cells.^[83] 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^[84] and is likely required for hybridization between species, which has been associated with major events in fungal evolution.^[85]

Evolution

Main article: Evolution of fungi

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.^[86] 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.^[87] Compression fossils are studied by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details.^[88]

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.^[89] 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.^[90] 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.^[91] 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.^[92] Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.^[93]

The fungi probably colonized the land during the Cambrian (542–488.3 Ma), long before land plants.^[94] 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.^[95] 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.^[94][96][97] At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,^[98] and all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299 Ma).^[99]

Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back to 635–551 Ma.^[100] Lichens were a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 400 Ma;^[101] this date corresponds to the age of the oldest known sporocarp fossil, a Paleopyrenomycites species found in the Rhynie Chert.^[102] The oldest fossil with microscopic features resembling modern-day basidiomycetes is Palaeoancistrus, found permineralized with a fern from the Pennsylvanian.^[103] 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 legletti) appeared during the mid-Cretaceous, 90 Ma.^[104][105]

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.^[106] However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess,^[107] the spike did not appear worldwide,^[108][109] and in many places it did not fall on the Permian-Triassic boundary.^[110]

Taxonomy

Unikonta	Amoebozoa Opisthokonta Animalia Choanozoa Nucleariids Fungi[37] Microsporidia Chytridiomycota Neocallimastigomycota Blastocladiomycota Zoopagomycotina Kickxellomycotina Entomophthoromycotina Mucoromycotina Glomeromycota Dikarya Ascomycota Basidiomycota

Even though traditionally included in many botany curricula and textbooks, fungi are now thought to be more closely related to animals than to plants and are placed with the animals in the monophyletic group of opisthokonts.^[111] Analyses using molecular phylogenetics support a monophyletic origin of the Fungi.^[37] The taxonomy of the 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.^[112]

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 nomenclature.^[37][113] 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 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.^[37] It recognizes seven phyla, two of which—the Ascomycota and the Basidiomycota—are contained within a branch representing subkingdom Dikarya. The below cladogram depicts the major fungal taxa and their relationship to opisthokont and unikont organisms. The lengths of the branches in this tree are not proportional to evolutionary distances.

Taxonomic groups

See also: List of fungal orders

The major phyla (sometimes called divisions) of fungi have been classified mainly on the basis of characteristics of their sexual reproductive structures. Currently, seven phyla are proposed: Microsporidia, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Glomeromycota, Ascomycota, and Basidiomycota.^[37]

Arbuscular mycorrhiza seen under microscope. Flax root cortical cells containing paired arbuscules.

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).^[91][114] 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.^[115] 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.^[37]

The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide. Chytrids produce zoospores that are capable of active movement through aqueous phases with a single flagellum, leading early taxonomists to classify them as protists. Molecular phylogenies, inferred from rRNA sequences in ribosomes, suggest that the Chytrids are a basal group divergent from the other fungal phyla, consisting of four major clades with suggestive evidence for paraphyly or possibly polyphyly.^[91]

The Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. Recent molecular data and ultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basidiomycota). The blastocladiomycetes are saprotrophs, feeding on decomposing organic matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids, which mostly exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis.^[91]

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 possibly in other terrestrial and aquatic environments. They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.^[37]

Members of the Glomeromycota form arbuscular mycorrhizae, a form of symbiosis where fungal hyphae invade plant root cells and both species benefit from the resulting increased supply of nutrients. All known Glomeromycota species reproduce asexually.^[68] The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago.^[116] 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.^[117] 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.^[37] 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.^[118] Medically relevant genera include Mucor, Rhizomucor, and Rhizopus.

Diagram of an apothecium (the typical cup-like reproductive structure of Ascomycetes) showing sterile tissues as well as developing and mature asci.

The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota.^[36] 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 mushrooms and truffles, single-celled yeasts (e.g., of the genera Saccharomyces, Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts. 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.^[119] 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).^[120]

Members of the Basidiomycota, commonly known as the club fungi or basidiomycetes, produce meiospores called basidiospores on club-like stalks called basidia. Most common mushrooms belong to this group, as well as rust and smut fungi, which are major pathogens of grains. Other important basidiomycetes include the maize pathogen Ustilago maydis,^[121] human commensal species of the genus Malassezia,^[122] and the opportunistic human pathogen, Cryptococcus neoformans.^[123]

Fungus-like organisms

Because of similarities in morphology and lifestyle, the slime molds (myxomycetes) and water molds (oomycetes) were formerly classified in the kingdom Fungi. Unlike true fungi the cell walls of these organisms contain cellulose and lack chitin. Slime molds are unikonts like fungi, but are grouped in the Amoebozoa. Water molds are diploid bikonts, grouped in the Chromalveolate kingdom. 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.^[124]

The nucleariids, currently grouped in the Choanozoa, may be a sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom.^[125]

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^[126] 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.^[127][128]

Symbiosis

Many fungi have important symbiotic relationships with organisms from most if not all Kingdoms.^{[129][130][131]} These interactions can be mutualistic or antagonistic in nature, or in the case of commensal fungi are of no apparent benefit or detriment to the host.^{[132][133][134]}

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.^[135]

The dark filaments are hyphae of the endophytic fungus Neotyphodium coenophialum in the intercellular spaces of tall fescue leaf sheath tissue

The mycorrhizal symbiosis is ancient, dating to at least 400 million years ago.^[116] 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.^[127][136] The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks".^[137] A special case of mycorrhiza is myco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont.^[138] Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.^[139] 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.^[140]

With algae and cyanobacteria

The lichen Lobaria pulmonaria, a symbiosis of fungal, algal, and cyanobacterial species

Lichens are formed by a symbiotic relationship between algae or cyanobacteria (referred to in lichen terminology as "photobionts") and fungi (mostly various species of ascomycetes and a few basidiomycetes), in which individual photobiont cells are embedded in a tissue formed by the fungus.^[141] Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession,^[142] and are the dominating life forms in extreme environments, including polar, alpine, and semiarid desert regions.^[143] They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves.^[144] As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis, while the fungus provides minerals and water. 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; around 20% of fungi—between 17,500 and 20,000 described species—are lichenized.^[145] Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of desiccation than most other photosynthetic organisms in the same habitat.^[146]

With insects

Many insects also engage in 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.^[147] Similarly, females of several wood wasp species (genus Sirex) inject their eggs together with spores of the wood-rotting fungus Amylostereum areolatum into the sapwood of pine trees; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae.^[148] Termites on the African savannah are also known to cultivate fungi,^[149] and yeasts of the genera Candida and Lachancea inhabit the gut of a wide range of insects, including neuropterans, beetles, and cockroaches; it is not known whether these fungi benefit their hosts.^[150]

As pathogens and parasites

The plant pathogen Aecidium magellanicum causes calafate rust, seen here on a Berberis shrub in Chile.

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,^[151] tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease,^[152] and Cryphonectria parasitica responsible for chestnut blight,^[153] and plant pathogens in the genera Fusarium, Ustilago, Alternaria, and Cochliobolus.^[133] Some carnivorous fungi, like Paecilomyces lilacinus, are predators of nematodes, which they capture using an array of specialized structures such as constricting rings or adhesive nets.^[154]

Some fungi can cause serious diseases in humans, several of which may be fatal if untreated. These include aspergilloses, candidoses, coccidioidomycosis, cryptococcosis, histoplasmosis, mycetomas, and paracoccidioidomycosis. Furthermore, persons with immuno-deficiencies are particularly susceptible to disease by genera such as Aspergillus, Candida, Cryptoccocus,^{[134][155][156]} Histoplasma,^[157] and Pneumocystis.^[158] Other fungi can attack eyes, nails, hair, and especially skin, the so-called dermatophytic and keratinophilic fungi, and cause local infections such as ringworm and athlete’s foot.^[159] Fungal spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic reactions.^[160]

Human use

Saccharomyces cerevisiae cells shown with DIC microscopy.

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 anti-cancer and cholesterol-lowering drugs. More recently, methods have been developed for genetic engineering of fungi,^[161] enabling metabolic engineering of fungal species. For example, genetic modification of yeast species^[162]—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.^[163]

Drugs

Many species produce metabolites that are major sources of 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 modification of the natural penicillins. Modern penicillins are semisynthetic compounds, obtained initially from fermentation cultures, but then structurally altered for specific desirable properties.^[164] Other antibiotics produced by fungi include: ciclosporin, commonly used as an immunosuppressant during transplant surgery; and fusidic acid, used to help control infection from methicillin-resistant Staphylococcus aureus bacteria.^[165] Widespread use of these antibiotics for the treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and many others began in the early 20th century and continues to play a major part in anti-bacterial chemotherapy. 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, and at low concentrations as quorum-sensing molecules for intra- or interspecies signaling.^[166]

Other drugs produced by fungi include griseofulvin isolated from Penicillium griseofulvum, used to treat fungal infections,^[167] 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 oyster mushroom.^[168]

Cultured foods

Baker's yeast or Saccharomyces cerevisiae, a single-celled fungus, is used to make bread and other wheat-based products, such as pizza dough and dumplings.^[169] Yeast species of the genus Saccharomyces are also used to produce alcoholic beverages through fermentation.^[170] Shoyu koji mold (Aspergillus oryzae) is an essential ingredient in brewing Shoyu (soy sauce) and sake, and the preparation of miso,^[171] while Rhizopus species are used for making tempeh.^[172] Several of these fungi are domesticated species that were bred or selected according to their capacity to ferment food without producing harmful mycotoxins (see below), which are produced by very closely related Aspergilli.^[173] Quorn, a meat substitute, is made from Fusarium venenatum.^[174]

Medicinal use

See also: Medicinal mushrooms

The medicinal fungi Ganoderma lucidum (left) and Cordyceps sinensis (right).

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 blazei,^[175][176] Ganoderma lucidum,^[177] and Cordyceps sinensis.^[178] Research has identified compounds produced by these and other fungi that have inhibitory biological effects against viruses^[179][180] and cancer cells.^[175][181] Specific metabolites, such as polysaccharide-K, ergotamine, and 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.^[182][183] In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from Trametes versicolor, is an approved adjuvant for cancer therapy.^[184]

Edible and poisonous species

Amanita phalloides accounts for the majority of fatal mushroom poisonings worldwide.

Edible mushrooms are well-known examples of fungi. Many are commercially raised, but others must be harvested from the wild. Agaricus bisporus, sold as button mushrooms when small or Portobello mushrooms when larger, is a commonly eaten species, 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.).^[185]

There are many more mushroom species that are harvested from the wild for personal consumption or commercial sale. Milk mushrooms, morels, chanterelles, truffles, 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.^[186]

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 color in cheeses such as Stilton or Roquefort, which are made by inoculation with Penicillium roqueforti.^[187] 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.^[188]

Stilton cheese veined with Penicillium roqueforti

Many mushroom species are poisonous to humans, with toxicities ranging from slight digestive problems or allergic reactions as well as hallucinations to severe organ failures and death. Genera with mushrooms containing deadly toxins include Conocybe, Galerina, Lepiota, and most infamously, Amanita.^[189] The latter genus includes the destroying angel (A. virosa) and the death cap (A. phalloides), the most common cause of deadly mushroom poisoning.^[190] The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.^[191] Tricholoma equestre was considered edible until being implicated in serious poisonings causing rhabdomyolysis.^[192] Fly agaric mushrooms (Amanita muscaria) also cause occasional non-fatal poisonings, mostly as a result of ingestion for use as a recreational drug for its hallucinogenic properties. Historically, fly agaric was used by different peoples in Europe and Asia and its present usage for religious or shamanic purposes is reported from some ethnic groups such as the Koryak people of north-eastern Siberia.^[193]

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.^[194][195]

Pest control

Grasshoppers killed by Beauveria bassiana

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,^[196] or if they are 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.^[197] 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.^[198] Examples that have been used as biological insecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella spp, Paecilomyces spp, and Verticillium lecanii.^[199][200] Endophytic fungi of grasses of the genus Neotyphodium, such as 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.^[201] Infecting cultivars of pasture or forage grasses with Neotyphodium endophytes is one approach being used in 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.^[202]

Bioremediation

See also: Mycoremediation

Certain fungi, in particular "white rot" fungi, can degrade insecticides, herbicides, pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, water, and basic elements.^[203] Fungi have been shown to biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.^{[204][205][206]}

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 who used the bread mold Neurospora crassa to test their biochemical theories.^[207] Other important model fungi are Aspergillus nidulans and the yeasts, Saccaromyces cerevisiae and Schizosaccharomyces pombe, each of which has 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 each address specific biological questions relevant to medicine, plant pathology, and industrial uses; examples include Candida albicans, a dimorphic, opportunistic human pathogen,^[208] Magnaporthe grisea, a plant pathogen,^[209] and Pichia pastoris, a yeast widely used for eukaryotic protein expression.^[210]

Others

Fungi are used extensively to produce industrial chemicals like citric, gluconic, lactic, and malic acids,^[211] and industrial enzymes, such as lipases used in biological detergents,^[212] cellulases used in making cellulosic ethanol^[213] and stonewashed jeans,^[214] and amylases,^[215] invertases, proteases and xylanases.^[216] Several species, most notably Psilocybin mushrooms (colloquially known as magic mushrooms), are ingested for their psychedelic properties, both recreationally and religiously.

Mycotoxins

Ergotamine, a major mycotoxin produced by Claviceps species, which if ingested can cause gangrene, convulsions, and hallucinations

Many fungi produce biologically active compounds, several of which are 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 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.^[217] Other notable mycotoxins include the aflatoxins, which are insidious 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.^[218]

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.^[219] Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory).^[220][221]

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 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.^[222]

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).^[223] 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.^[224]

History

Mycology is a relatively new science that became systematic after the development of the microscope in the 16th 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.^[225] Micheli not only observed spores, but showed that under the proper conditions, they could be induced into growing into the same species of fungi from which they originated.^[226] Extending the use of the 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 so as to be considered a founder of modern mycology. Later, Elias Magnus Fries (1794–1878) further elaborated the classification of fungi, using spore color and various 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 and Charles Tulasne, Arthur H. R. Buller, Curtis G. Lloyd, and Pier Andrea Saccardo. The 20th century has seen a modernization of mycology that has come from advances in biochemistry, genetics, molecular biology, and biotechnology. The use of DNA sequencing technologies and phylogenetic analysis has provided new insights into fungal relationships and biodiversity, and has challenged traditional morphology-based groupings in fungal taxonomy.^[227]

See also

Fungi portal

• MycoBank
• Plant pathology

Footnotes

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References

• Ainsworth GC. (1976). Introduction to the History of Mycology. Cambridge, UK: Cambridge University Press. ISBN 0-521-11295-8.
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• Tree of Life web project: Fungi
• Fungus at the Encyclopedia of Life

Opisthokont: Fungi classification, fungal orders Dikarya Ascomycota saccharomyceta Pezizomycotina leotiomyceta Geoglossomycetes · dothideomyceta (Arthoniomycetes/ Dothideomycetes) · Eurotiomycetes · Lecanoromycetes · sordariomyceta ((Leotiomycetes (Sordariomycetes/ Laboulbeniomycetes)) · Lichinomycetes Other Orbiliomycetes · Pezizomycetes Saccharomycotina Saccharomycetes Taphrinomycotina Neolectomycetes · Pneumocystidomycetes · Schizosaccharomycetes · Taphrinomycetes Basidiomycota Pucciniomycotina · Ustilaginomycotina · Agaricomycotina · Urediniomycetes Glomeromycota Glomerales · Diversisporales · Paraglomerales · Archaeosporales Zygomycota Mucoromycotina Endogonales · Mucorales (Chaetocladiaceae, Choanephoraceae, Cunninghamellaceae, Gilbertellaceae, Mortierellaceae, Mucoraceae, Mycotyphaceae, Phycomycetaceae, Pilobolaceae, Radiomycetaceae, Saksenaeaceae, Syncephalastraceae, Thamnidiaceae, Umbelopsidaceae) · Mortierellales Entomophthoromycotina Entomophthorales (Basidiobolaceae, Ancylistaceae) Kickxellomycotina Asellariales · Kickxellales · Dimargaritales · Harpellales Zoopagomycotina Zoopagales Other Blastocladiomycota · Chytridiomycota/Neocallimastigomycota · Microsporidia : MYC , drug ()

Microbiology: Fungus Structure Reproduction/spore teleomorph/sexual: Zygospore · Ascospore/Ascus · Basidiospore/Basidium/Teliospore anamorph/asexual: Sporangium · Conidium · Chlamydospore · Oidium · Pycniospores Other Hypha · Haustorium · Mycelium · Cell wall Growth patterns Dimorphic fungi · Mold · Yeast · Mushroom : MYC , drug ()

Eukaryota classification Domain : Archaea · Bacteria · Eukaryota Bikonta AH/SAR AH Archaeplastida, or Plantae sensu lato Viridiplantae/Plantae sensu stricto · Rhodophyta · Glaucocystophyceae Hacrobia, or non-SAR chromalveolata Haptophyta · Cryptophyta · Centroheliozoa SAR Halvaria Heterokont ("S") Ochrophyta · Bigyra · Pseudofungi Alveolata Ciliates · Myzozoa (Apicomplexa, Dinoflagellata) Rhizaria Cercozoa · Retaria (Foraminifera, Radiolaria) Excavata Discoba (Euglenozoa, Percolozoa) · Metamonad · Malawimonas Apusozoa Apusomonadida (Apusomonas, Amastigomonas) · Ancyromonadida (Ancyromonas) · Hemimastigida (Hemimastix, Spironema, Stereonema) Unikonta Amoebozoa Lobosea · Conosa · Phalansterium Opisthokonta Holozoa Mesomycetozoea Dermocystida · Ichthyophonida Filozoa Filasterea Capsaspora · Ministeria Choanoflagellatea Codonosigidae Metazoa or "Animalia" Eumetazoa (Bilateria, Cnidaria, Ctenophora) · Mesozoa · Parazoa (Placozoa, Porifera) Holomycota Fungi Dikarya (Ascomycota, Basidiomycota) · Glomeromycota · Zygomycota · Blastocladiomycota · Chytridiomycota/Neocallimastigomycota · Microsporidia Nucleariidae Nuclearia · Micronuclearia

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