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A fungus is any member of a large group of organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. The Fungi (pronounced or /'f??ga?/) are classified as a kingdom that is separate from plants and animals. One major difference is that fungal cells have cell walls that contain chitin, unlike the cell walls of plants, which contain cellulose. These and other differences show that the fungi form a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (a monophyletic group). This fungal group is distinct from the structurally similar slime molds (myxomycetes) and water molds (oomycetes). The discipline of biology devoted to the study of fungi is known as mycology, which is often regarded as a branch of botany, even though geneti c studies have shown that fungi are more closely related to animals than to plants. Fungi reproduce via spores, which are often produced on specialized structures or in fruiting bodies, such as the head of a mushroom.

Abundant worldwide, most fungi are invisible to the naked eye because of their very small size. They live mainly in soil, on dead matter, and as symbionts of plants, animals, or other fungi. They perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange. Fungi may become noticeable when fruiting, either as mushrooms or molds. They have long been used as a direct source of food, such as mushrooms and truffles, as a leavening agent for bread, and in fermentation of various food products, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially an d in detergents. Fungi are also used as biological agents to control weeds and pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals including humans. The fruiting structures of a few species are consumed recreationally or in traditional ceremonies as a source of psychotropic compounds. 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.

Etymology

The English word fungus is directly adopted from the Latin fungus (mushroom), used in the writings of Horace and Pliny.< sup id="cite_ref-2" class="reference">[3] This in turn is derived from the Greek word sphongos/sf????? ("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/µ???? (mushroom) and logos/????? (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, based largely on 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. Both plants and fungi possess a cell wall, a feature absent in the Animal Kingdom. 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] Many studies have identified distinct morphological, biochemical, and genetic features in the Fungi that clearly separate them from the other kingdoms. The fungal kingdom is defined by several features—some shared with other organisms, others unique to the fungi:

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.^[7] 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., g lycogen, which is also found in animals^[8]).
• With animals: Fungi lack chloroplasts and are heterotrophic organisms, requiring preformed organic compounds as energy sources.^[9]
• With plants: Fungi possess a cell wall^[10] and vacuoles.^[11] 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.^[12]
• With euglenoids and bacteria: Higher fungi, euglenoids, a nd some bacteria produce the amino acid L-lysine in specific biosynthesis steps, called the a-aminoadipate pathway.^[13][14]
• The cells of most fungi grow as tubular, elongated, and thread-like 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.^[15] Both fungi and oomycetes grow as filamentous hyphal cells.^[16] In contrast, similar-looking organisms, such as filamentous green algae, grow b y repeated cell division within a chain of cells.^[8]

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.^[17]
• 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,^[18][19] fungi are the only organisms that combine these two structural molecules in their cell wall. In contrast to plants and the oomycetes, fu ngal cell walls do not contain cellulose.^[20]

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,^[21] that resemble and perform functions similar to the roots of pl ants.

Characteristics shared with plants also include a biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as chemical building blocks.^[22] However, plants have an additional terpene pathway in their chloroplasts, a structure fungi do not possess.^[23] Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants.^[22] 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][22] In common with some plant and animal species, more than 60 fungal species display the phenomenon of bioluminescence.^[25]

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^[26] or ionizing radiation,^[27] as well as in deep sea sediments.^[28] Some can survive the intense UV and cosmic radiation encountered during space travel.^[29] Most grow in terrestrial environments, but several species live partly or solely in aquatic habitats, such as the chytrid fungus Batrachochytrium dendrobatidis, which 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.^[30] Other examples include fungi living in hydrothermal areas of the ocean. ^[31]

Around 100,000 species of fungi have been formally described by taxonomists,^[32] but the true dimension of global fungal diversity is not well understood.^[33] Based on 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.^[34] In mycology, species have historically been distinguished using a variety of species concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.^[35] 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.^[36]

Morphology

Microscopic Structures

A hypha of Hyaloperonospora parasitica (downy mildew) growing within the leaf tissue of Arabidopsis thaliana. The long structure is the hypha, and the little spheres are haustoria, which extract nutrients from the plant cells.

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 tips typically form by branching from sub-apical hyphal locations or occasionally by bifurcation (forking) of growing tips.^[37] The combination of apical growth and branching/forking leads to the development of a mycelium, an interconnected network of hyphae.^[38] Hyphae can be septate, i.e., divided into compartments separated by cross walls (septa), each compartment containing one or more nuclei, or can be coenocytic, i.e., lacking hyphal compartmentalization.^[39] Septa have pores, such as the dolipore septa in the basidiomycetes that allow cytoplasm, organelles, and sometimes nuclei to pass through.^[40] Coenocytic hyphae are essentially multinucleate supercells.^[41] Many species have developed specialized hyphal structures for nutrient upta ke from living hosts; examples include haustoria in plant parasites of most phyla, and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients.^[42]

Although fungi are part of the opisthokont clade—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, besides glucans (e.g., ß-1,3-glucan) and other typical components, contains the biopolymer chitin.^[44]

Macroscopic Structu res

Armillaria ostoyae

Fungal mycelia can become visible macroscopically, for example, as concentric rings on various surfaces, such as damp walls, and on other substrates, such as spoilt food, and are commonly and generically called mold (British spelling, mould); mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies, exhibiting characteristic macroscopic growth shapes and colors, due to spores or pigmentation.^[45] Some individual fungal colonies can grow to a very large size and mass, in some cases reaching 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]

In the ascomycetes, a specialized structure important in sexual reproduction is the apothecium, a cup-shaped structure 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 are well-known as mushrooms.

Growth and Physiology

The growth of fungi as filamentous 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 MPa (80& #160;bars).^[50] The filamentous fungus Paecilomyces lilacinus uses a similar structure to penetrate the eggs of plant-parasitic 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] While the vast majority of filamentous (hypha-forming) fungi grow in a polar or directional fashion by extension at the tip of the hypha,^[56] intercalary extension as in the case of some endophytic fungi,^[57] or by volume expansion during the development of mushroom stipes and other large organs^[58] are alternative forms of growth. Growth of fungi as multicellular structures consisting of somatic and reproductive cells—as seen and 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 remarkable 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] A few species seem to be able to utilize the pigment melanin to extract energy from ionizing radiation, such as gamma radiation, for "radiotrophic" growth.^[27] This process might bear similarity to CO₂ fixation via anaplerotic reactions using visible light, but instead utilizing ionizing radiation as a source of energy.^[63]

Reproduction

Polyporus squamosus

Fungal reproduction is complex, reflecting the heterogeneity in lifestyles and genetic makeup within this Kingdom of organisms.^[64] It is estimated that a third of all fungi use more than one type of reproduction, frequently in t wo well-differentiated life cycle stages (the teleomorph and the anamorph).^[65] Environmental conditions trigger genetically determined developmental programs that lead to the creation of specialized structures for sexual or asexual reproduction. These structures aid both reproduction and efficient dispersal of spores or spore-containing propagules.

Asexual Reproduction

Asexual reproduction via vegetative spores or through mycelial fragmentation is common; it maintains clonal populations adapted to a specific niche, and allows more rapid dispersal than sexual reproduction.^[66] In the case of the "Fungi imperfecti" or Deuteromycota, which lack a sexual cycle, it is the only means of propagation.

Sexual Reproduction

Sexual reproduction with meiosis exists in all fungal phyla (with the exception of the Glomeromycota).^[67] 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 based on morphological differences in sexual structures and reproductive strategies.^[68][69] Mating experiments between fungal isolates may identify species based on biological species concepts.^[69] 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.^[70]

Most fungi have both a 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).^[71]

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 in to 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.^[72]

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 dika ryotic stage with two genetically different nuclei in each hyphal compartment.^[73] A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.^[74] 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 i nto new genetically identical haploid fungal mycelia.^[75]

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.^[76] 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.^[77] 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;^[78] the net result is that the spore is ejected 0.01–0.02 cm, sufficient distance for it to fall through the g ills or pores into the air below.^[79] 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.^[80] Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.^[81]

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.^[82] 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^[83] and is likely required for hybridization between species, which has been associated with major events in fungal evolution.^[84]

Evolution

In contrast to plants and animals, the early fossil record of the fungi is meager. Factors that likely contribute to the under-r epresentation 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.^[85] 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.^[86] Compression fossils are studied by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details.^[87]

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.^[88] More recent studies (2009) estimate the arrival of fungal organisms at about 760–1060 Ma based on comparisons of the rate of evolution in closely related groups.^[89] 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.^[90] 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.^[91] Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.^[92]

The fungi probably colonized the land during the Cambrian (542–488.3 Ma), long before land plants.^[93] Fossilized hyphae and spores recovered from the Ordovician of Wisco nsin (460 Ma) resemble modern-day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like plants.^[94] 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.^[95][93][96] At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,^[97] and all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299 Ma).^[98]

Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back to 635–551 Ma.^[99] Lichens were a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 400 Ma;^[100] this date corresponds to the age of the oldest known sporocarp fossil, a Paleopyrenomycites species found in the Rhynie Chert.^[101] The oldest fossil with microscopic features resembling modern-day basidiomycetes is Palaeoancistr us, found permineralized with a fern from the Pennsylvanian.^[102] Rare in the fossil record are the homobasidiomycetes (a taxon roughly equivalent to the mushroom-producing species of the agaricomycetes). Based on two amber-preserved specimens, the earliest known mushroom-forming fungi (the extinct species Archaeomarasmius legletti) appeared during the mid-Cretaceous, 90 Ma.^[103][104]

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.^[105] However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess,^[106] the spike did not appear worldwide,^[107][108] and in many places it did not fall on the Permian-Triassic boundary.^[109]

Taxonomy

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.^[110] Analyses using molecular phylogenetics support a monophyletic origin of the Fungi.^[36] 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 concep ts obtained from experimental matings.^[111]

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.^[36][112] 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.^[36] 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

The major phyla (sometimes called divisions) of fungi have been classified based mainly on the characteristics of their sexual reproductive structures. Currently, seven phyla are proposed: Microsporidia, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Neocallimastigomycota, Glo meromycota, Ascomycota, and Basidiomycota.^[36]

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

Phylogenetic analysis has demonstrated conclusively that the Microsporidia, unicellular parasites of animals and protists, are fairly recent and highly derived endobiotic fungi (living within the tissue of another species),^{[113][90][114]} and they were given phylum status in 2007.^[36]

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.^[90]

The B lastocladiomycota 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 Basiomycota). 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.^[90]

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 rela ted chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.^[36]

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.^[67] The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago.^[115] 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. ^[116] 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.^[36] 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.^[117] 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. 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 t he 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. 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).^[118]

Members of the Basidiomycota, commonly known as the club fungi or basidiomycetes, produce meiospores called basidiospores o n 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, human commensal species of the genus Malassezia, and the opportunistic human pathogen, Cryptococcus neoformans.

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.^[119]

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.^[120]

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^[121] 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.^[122][123]

Symbiosis

Many fungi have important symbiotic relationships with organisms from most if not all Kingdoms.^{[124][125][126]} 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.^{[127][128][129]}

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 surviv al.^[130]

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.^[115] 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.^[122][131] The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks".^[132] Some species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.^[133] 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.^[134]

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.^[135] Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession, ^[136] and are the dominating life forms in extreme environments, including polar, alpine, and semiarid desert regions.^[137] They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves.^[138] As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis, while the fungus provides mineral s 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.^[139] 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 dessication than most other photosynthetic organisms in the same habitat.^[140]

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.^[141] 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.^[142] Termites on the African savannah are also known to cultivate fungi,^[143] 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.^[144]

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,^[145] tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease,^[146] and Cryphonectria parasitica responsible for chestnut blight,^[147] and plant pathogens in the genera Fusarium, < i>Ustilago, Alternaria, and Cochliobolus.^[128] 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.^[148]

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,^{[129][149][150]} Histoplasma,^[151] and Pneumocystis.^[152] Other fungi can attack eyes, nails, hair, and especially skin, the so-called dermatophytic and keratinophilic fungi,^[153] 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.^[154]

Human U.S.A.

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 imp act 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,^[155] enabling metabolic engineering of fungal species. For example, genetic modification of yeast species^[156]—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.^[157]

Antibiotics

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 ß-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.^[158] Other antibiotics produced by fungi include: griseofulvin from Penicillium griseofulvin used to treat dermatophyte infections of the skin, hair and nails;^[159] cyclosporins, commonly used as an immunosuppressant during transplant surgery; and fusidic acid, used to help control infection from methicillin-resistant Staphylococcus aureus bacteria.^[160] 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.^[161]

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.^[162] Yeast species of the genus Saccharomyces are also used to produce alcoholic beverages through fermentation.^{[163]< /a>} Shoyu koji mold (Aspergillus oryzae) is an essential ingredient in brewing Shoyu (soy sauce) and sake, and the preparation of miso,^[164] while Rhizopus species are used for making tempeh.^[165] Several of these fungi are domesticated species that were bred or selected based on their capacity to ferment food without producing harmful mycotoxins (see below), which are produced by very closely related Aspergilli.^[166] Quorn, a meat substitute, is made from Fusarium venenatum.^[167]

Medicinal U.S.A.

Certain mushrooms enjoy usage as therapeutics in traditional and folk medicines, such as Traditional Chinese medicine. Notable species with a well-documented history of use include Agaricus blazei,^[168][169] Ganoderma lucidum,^[170] and Cordyceps sinensis.^[171] Research has identified compounds produced by these and other fungi that have inhibitory biological effects against viruses^[172][173] and cancer cells.^[174][168] Specific metabolites with biological or antimicrobial activities, such as polysaccharide-K, ergotamine, and ß-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.^[175][176] In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from Trametes versicolor, is an approved adjuvant for cancer therapy.^[177]

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.).^[178]

There are man y 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.^[179]

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.^[180] 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 a ccumulate due to growth of other fungi during cheese ripening or storage.^[181]

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. The most deadly mushrooms belong to the genera Inocybe, Cortinarius, and most infamously, Amanita. The latter genus includes the destroying angel (A. virosa) and the de ath cap (A. phalloides), the most common cause of deadly mushroom poisoning.^[182] The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.^[183] Tricholoma equestre was considered edible until being implicated in serious poisonings causing rhabdomyolysis.^[184] 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 Europ e 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.^[185]

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.^[186][187]

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,^[188] 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.^[189] This has genera ted 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.^[190] Examples that have been used as biological insecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella spp, Paecilomyces spp, and Verticillium lecanii.^[191][192] 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.^[193] 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.^[194]

Bioremediation

Certain fungi, in particular "white rot" fungi, can degrade insecticides, herbicides, pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, w ater, and basic elements.^[195] Fungi have been shown to biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.^{[196][197][198]}

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 c rassa to test their biochemical theories.^[199] 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,^[200] Magnaporthe grisea, a plant pathogen,^[201] and Pichia pastoris, a yeast widely used for eukaryotic protein expression.^[202]

[edit] Others

Fungi are used extensively to produce industrial chemicals like citric, gluconic, lactic, and malic acids, antibiotics, and even to make stonewashed jeans.^[203] Fungi are also sources of industrial enzymes, such as lipases used in biological detergents,^[204] amylases,^[205] cellulases,^[206] invertases, proteases and xylanases.^[207] Several species, most notably Psilocybin mushrooms (colloquially known as magic mushrooms), are ingested for their psychedelic properties, both recreationally and religiously.

[edit] 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.^[208] 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.^[209]

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.^[210] Mycotoxins may provide fitness benefits in terms of physiological adaptati on, competition with other microbes and fungi, and protection from consumption (fungivory).^[211][212]

[edit] 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 most plan t pathogens are fungi.

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).^[213] 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.^[214]

[edit] 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.^[215] 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.^[216] 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 twentieth 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.^[217]

The Kingdom Fungi is a member of the Domain Eukaryota. Here is the complete "parentage" of Fungi:

• Domain: Eukaryota Whittaker & Margulis,1978 - eukaryotes
  • Kingdom: Fungi (Linnaeus, 1753) Nees, 1817