Fungus

{{Short description|Organism belonging to kingdom Fungi}} {{Redirect|Fungi|other uses|Fungi (disambiguation)|and|Fungus (disambiguation)}} {{Featured article}} {{pp-move}} {{protection padlock|small=yes}} {{Use dmy dates|date=August 2023}} {{Use American English|date=September 2025}} {{cs1 config |name-list-style=vanc |display-authors=6}}

{{Automatic taxobox | name = Fungi | fossil_range = Middle Ordovician – Present (but see text) {{Fossilrange|460|0|earliest=Ediacaran}} | image = Fungi_collage.jpg | image_upright = 1.3 | image_caption = Clockwise from top left: {{plainlist| * ''Amanita muscaria'', a basidiomycete; * ''Sarcoscypha coccinea'', an ascomycete; * bread covered in mold; * a chytrid; * an ''Aspergillus'' conidiophore. }} | image_alt = A collage of five fungi (clockwise from top left): a mushroom with a flat red top with white spots and a white stem growing on the ground; a red cup-shaped fungus growing on wood; a stack of green and white moldy bread slices on a plate; a microscopic spherical grey semitransparent cell with a smaller spherical cell beside it; a microscopic view of an elongated cellular structure shaped like a microphone, attached to the larger end is a number of smaller roughly circular elements that collectively form a mass around it | display_parents = 6 | taxon = Fungi | authority = R.T.Moore (1980)<ref name=Moore1980/><ref>{{cite web |title=Record Details: Fungi R.T. Moore, Bot. Mar. 23(6): 371 (1980) |url=https://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=90154 |publisher=Index Fungorum |access-date=18 June 2024 |archive-date=18 June 2024 |archive-url=https://web.archive.org/web/20240618201249/https://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=90154 |url-status=live }}</ref> | subdivision_ranks = Subkingdoms/phyla | subdivision = * Rozellomyceta ** Rozellomycota *** Microsporidia * Aphelidiomyceta ** Aphelidiomycota * "Eumycota"{{efn|name=eumycota|This reflects a modern sense of "{{vanchor|Eumycota}}", which is sister to Aphelidiomyceta. It is distinct from the older sense used to separate fungi (now simply the kingdom "Fungi") from slime molds and water molds. The current "Eumycota" matches the protistologist's definition of Fungi as an exclusively osmotrophic lineage.<ref name=Hyde2024/>}} ** Chytridiomyceta *** Neocallimastigomycota *** Monoblepharomycota *** Chytridiomycota ** Blastocladiomyceta *** Blastocladiomycota *** Sanchytriomycota<ref name=Galindo2021/><ref name=Hyde2024/> ** Amastigomycota *** Basidiobolomyceta **** Basidiobolomycota *** Olpidiomyceta **** Olpidiomycota *** Zoopagomyceta **** Zoopagomycota **** Entomophthoromycota **** Kickxellomycota *** Mortierellomyceta **** Mortierellomycota *** Mucoromyceta (possibly paraphyletic)<ref name=Wijayawardene2024/> **** Calcarisporiellomycota **** Mucoromycota **** Mortierellomycota{{efn|Alternatively, included in Mucoromycota as a subphylum.}} **** Glomeromycota{{efn|Alternatively, included in Mucoromycota as a subphylum. In rRNA-based analysis, groups with Dikarya to form Symbiomycota.}} *** Dikarya **** Entorrhizomycota **** Basidiomycota **** Ascomycota }}

A '''fungus''' ({{plural form}}: fungi{{efn|{{IPAc-en|audio=En-us-fungi.ogg|ˈ|f|ʌ|n|dʒ|aɪ}}, {{IPAc-en|audio=En-us-fungi-2.ogg|ˈ|f|ʌ|ŋ|ɡ|aɪ}}, {{IPAc-en|audio=En-us-fungi-3.ogg|ˈ|f|ʌ|ŋ|ɡ|i}}, or {{IPAc-en|audio=En-us-fungi-4.ogg|ˈ|f|ʌ|n|dʒ|i}}{{efn|name=pronunciation|The first two pronunciations are favored more in the US and the others in the UK, however all pronunciations can be heard in any English-speaking country.}}}} or funguses<ref name="OxfordDictionary"/>) is any member of the group of eukaryotic organisms that includes yeasts, molds, as well as mushrooms. These organisms are classified in the biological kingdom '''Fungi'''.<!-- keep bold formatting for redirect --><ref name=Whittaker1969/><ref name=CavalierSmith1998/>

A characteristic that places fungus in a different kingdom from plants, bacteria, and some protists is having chitin in their cell walls. Fungi, like animals, are heterotrophs: they acquire their nutrition by absorbing dissolved organic molecules, typically by secreting digestive enzymes into their environment. A fungus does not perform photosynthesis. Growth is their means of motility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the ''Eumycota'' (''true fungi'' or ''Eumycetes''), that share a common ancestor (i.e. they form a ''monophyletic group''), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is called mycology (from the Greek {{Lang|grc|μύκης}}, {{translit|grc|mykes}} {{gloss|mushroom}}). In the past, mycology was regarded as a branch of botany, although it is now known that fungi are genetically more closely related to animals than to plants.

Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment. Over 90% of plants are dependent on Mycorrhizal symbiosis between plants and fungi<ref name=Bonfante2003/> and this process also enhances photosynthesis in plants, increasing carbon uptake from the atmosphere and helping to stop climate change.<ref name=Paul/>

Fungi have long been used as a direct source of human food, in the form of mushrooms and truffles; as a leavening agent for bread; and in the fermentation of various food products, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control weeds, plant diseases, and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals, including humans. The fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g., rice blast disease) or food spoilage can have a large impact on human food supplies and local economies. Fungi are threatened by fungicides, pesticides, pollution, deforestation and more.<ref name=Paul/>

The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of the fungus kingdom, which has been estimated at 2.2&nbsp;million to 3.8&nbsp;million species.<ref name=Lucking2017/> Of these, only about 148,000 have been described,<ref name="Cheek et al. 2020"/> with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans.<ref>{{cite journal |title=Stop neglecting fungi |date=25 July 2017 |journal=Nature Microbiology |volume=2 |issue=8 |article-number=17120 |doi=10.1038/nmicrobiol.2017.120 |doi-access=free |title-link=doi |pmid=28741610 |bibcode=2017NatMb...217120. }}</ref> Ever since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christiaan 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 first decade of the 21st century have helped reshape the classification within the fungi kingdom, which is divided into one subkingdom, seven phyla, and ten subphyla. {{toclimit}}

==Etymology== The English word ''fungus'' is directly adopted from the Latin {{wikt-lang|la|fungus}} {{gloss|mushroom}}, used in the writings of Horace and Pliny.<ref name=Simpson1979/> This in turn is derived from the Greek word {{translit|grc|sphongos}} ({{wikt-lang|grc|σφόγγος}} {{gloss|sponge}}), which refers to the macroscopic structures and morphology of mushrooms and molds;{{sfn|Ainsworth|1976|p=2}} the root is also used in other languages, such as the German {{wikt-lang|de|Schwamm}} {{gloss|sponge}} and {{wikt-lang|de|Schimmel}} {{gloss|mold}}.<ref name="Mitzka1960"/>

The word ''mycology'' is derived from the Greek {{Transliteration|grc|mykes}} ({{wikt-lang|grc|μύκης}} {{gloss|mushroom}}) and {{translit|grc|logos}} ({{wikt-lang|grc|λόγος}} {{gloss|discourse}}).{{sfn|Alexopoulos|Mims|Blackwell|1996|p=1}} It denotes the scientific study of fungi. The Latin adjectival form of "mycology" ({{lang|la|mycologicæ}}) appeared as early as 1796 in a book on the subject by Christiaan Hendrik Persoon.<ref name=Persoon1796/> The word appeared in English as early as 1824 in a book by Robert Kaye Greville.<ref name=Greville1824/> In 1836 the English naturalist Miles Joseph Berkeley's publication ''The English Flora of Sir James Edward Smith, Vol. 5.'' also refers to mycology as the study of fungi.{{sfn|Ainsworth|1976|p=2}}<ref name=Smith1836/>

A group of all the fungi present in a particular region is known as ''mycobiota'' (plural noun, no singular).<ref>{{cite web |url=http://glossary.lias.net/wiki/Mycobiota |title=LIAS Glossary |access-date=14 August 2013 |archive-url=https://web.archive.org/web/20131211113036/http://glossary.lias.net/wiki/Mycobiota |archive-date=11 December 2013 |url-status=live}}</ref> The term ''mycota'' is often used for this purpose, but many authors use it as a synonym of fungi. The word ''funga'' has been proposed as a less ambiguous term morphologically similar to fauna and flora.<ref name="Kuhar et al. 2018"/> The Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN) in August 2021 asked that the phrase ''fauna and flora'' be replaced by ''fauna, flora, and funga''.<ref>{{cite web |url=https://www.iucn.org/sites/dev/files/statement-3f.pdf |title=IUCN SSC acceptance of Fauna Flora Funga |publisher=Fungal Conservation Committee, IUCN SSC |date=2021 |quote=The IUCN Species Survival Commission calls for the due recognition of fungi as major components of biodiversity in legislation and policy. It fully endorses the Fauna Flora Funga Initiative and asks that the phrases '''animals and plants''' and '''fauna and flora''' be replaced with '''animals, fungi, and plants''' and '''fauna, flora, and funga'''. |access-date=11 November 2021 |archive-date=11 November 2021 |archive-url=https://web.archive.org/web/20211111141833/https://www.iucn.org/sites/dev/files/statement-3f.pdf }}</ref>

==Characteristics== [[File:HYPHAE.png|thumb|upright=1.35|'''Fungal hyphae cells''' {{image key |list type=ordered |Hyphal wall |Septum |Mitochondrion |Vacuole |Ergosterol crystal |Ribosome |Nucleus |Endoplasmic reticulum |Lipid body |Plasma membrane |Spitzenkörper |Golgi apparatus }} ]] [[File:Fungus cell cycle-en.svg|thumb|upright=1.35|Fungal cell cycle showing dikaryons typical of higher fungi]] 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 habit. Although inaccurate, the common misconception that fungi are plants persists among the general public due to their historical classification, as well as several similarities.<ref>{{cite web |url=https://www.researchgate.net/publication/26571382 |title=Fifth-Grade Elementary School Students' Conceptions and Misconceptions about the Fungus Kingdom |access-date=5 October 2022}}</ref><ref>{{cite web |url=https://www.cpp.edu/respect/resources/documents_kinder/pa_lessons_1-3/resources/gr0.kpa_common_student_ideas.pdf |title=Common Student Ideas about Plants and Animals |access-date=5 October 2022 |archive-date=26 March 2023 |archive-url=https://web.archive.org/web/20230326043113/https://www.cpp.edu/respect/resources/documents_kinder/pa_lessons_1-3/resources/gr0.kpa_common_student_ideas.pdf |url-status=live }}</ref> Like plants, fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit bodies, which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago (around the start of the Neoproterozoic Era).<ref name=Bruns2006/><ref name="Baldauf1993"/> Some morphological, biochemical, and genetic features are shared with other organisms, while others are unique to the fungi, clearly separating them from the other kingdoms:

Shared features: * With other eukaryotes: Fungal cells contain membrane-bound nuclei with chromosomes that contain DNA with noncoding regions called introns and coding regions called exons. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes, and ribosomes of the 80S type.{{sfn|Deacon|2005|p=4}} 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{{sfn|Deacon|2005|pp=128–129}}). * With animals: Fungi lack chloroplasts and are heterotrophic organisms and so require preformed organic compounds as energy sources.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=28–33}} * With plants: Fungi have a cell wall{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=31–32}} and vacuoles.<ref name=Shoji2006/> 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.{{sfn|Deacon|2005|p=58}} * With euglenoids and bacteria: Higher fungi, euglenoids, and some bacteria produce the amino acid <small>L</small>-lysine in specific biosynthesis steps, called the α-aminoadipate pathway.<ref name=Zabriskie2000/><ref name=Xu2006/> * In common with some plant and animal species, more than one hundred fungal species display bioluminescence.<ref name="Desjardin 2010"/>

Unique features: * The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures called hyphae, which may contain multiple nuclei and extend by growing at their tips. Each tip contains a set of aggregated vesicles—cellular structures consisting of proteins, lipids, and other organic molecules—called the Spitzenkörper.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=27–28}} Both fungi and oomycetes grow as filamentous hyphal cells.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=685}} In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells.{{sfn|Deacon|2005|pp=128–129}} * Some species grow as unicellular yeasts that do not form hyphae and reproduce by budding or fission. Dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=30}} * The fungal cell wall is made of a chitin-glucan complex; while glucans are also found in plants and chitin in the exoskeleton of arthropods,{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=32–33}} fungi are the only organisms that combine these two structural molecules in their cell wall. Unlike those of plants and oomycetes, fungal cell walls do not contain cellulose.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=33}}<ref name="Gow et al. 2017"/>

[[File:Omphalotus nidiformis Binnamittalong 2 email.jpg|thumb|right|alt=A whitish fan or funnel-shaped mushroom growing at the base of a tree.|''Omphalotus nidiformis'', a bioluminescent mushroom]] Most fungi lack an efficient system for the long-distance transport of water and nutrients, such as the xylem and phloem in many plants. To overcome this limitation, some fungi, such as ''Armillaria'', form rhizomorphs,<ref name=Mikhail2005/> which resemble and perform functions similar to the roots of plants. As eukaryotes, fungi possess a biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as chemical building blocks.<ref name=Keller2005/> Plants and some other organisms have an additional terpene biosynthesis pathway in their chloroplasts, a structure that fungi and animals do not have.<ref name=Wu2007/> Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants.<ref name=Keller2005/> 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 convergent evolution of these enzymes in the fungi and plants.<ref name=Keller2005/><ref name=Tudzynski2005/>

==Diversity== [[File:Fungus in a Wood.JPG|thumb|Bracket fungi on a tree stump]]

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<ref name=Vaupotic2008/> or ionizing radiation,<ref name=Dadachova2007/> as well as in deep sea sediments.<ref name=Raghukumar1998/> Some can survive the intense UV and cosmic radiation encountered during space travel.<ref name=Sancho2007/> Most grow in terrestrial environments, though several species live partly or solely in aquatic habitats, such as the chytrid fungi ''Batrachochytrium dendrobatidis'' and ''B.&nbsp;salamandrivorans'', parasites that have been responsible for a worldwide decline in amphibian populations. These organisms spend part of their life cycle as a motile zoospore, enabling them to propel themselves through water and enter their amphibian host.<ref name="Fisher et al. 2020"/> Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.<ref name="Vargas-Gastélum & Riquelme 2020"/>

[[File:White fungus in wood chips.jpg|thumb|left|Widespread white fungus in wood chip mulch in an Oklahoma garden<ref>{{cite web |title=Fungi in Mulches and Composts |url=https://ag.umass.edu/landscape/fact-sheets/fungi-in-mulches-composts |website=University of Massachusetts Amherst |date=6 March 2015 |access-date=15 December 2022 |archive-date=15 December 2022 |archive-url=https://web.archive.org/web/20221215220016/https://ag.umass.edu/landscape/fact-sheets/fungi-in-mulches-composts |url-status=live }}</ref>]] {{As of|2020|post=,}} around 148,000 species of fungi have been described by taxonomists,<ref name="Cheek et al. 2020"/> but the global biodiversity of the fungus kingdom is not fully understood.<ref name=Mueller2006/> A 2017 estimate suggests there may be between 2.2 and 3.8&nbsp;million species.<ref name=Lucking2017/> The number of new fungi species discovered yearly has increased from 1,000 to 1,500 per year about 10 years ago, to about 2,000 with a peak of more than 2,500 species in 2016. In the year 2019, 1,882 new species of fungi were described, and it was estimated that more than 90% of fungi remain unknown.<ref name="Cheek et al. 2020"/> The following year, 2,905 new species were described—the highest annual record of new fungus names.<ref name="Wang et al. 2021"/> 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.{{sfn|Kirk|Cannon|Minter|Stalpers|2008|p=489}} 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.<ref name=Hibbett2007/>

==Mycology== {{Main|Mycology}} [[File:Pier Antonio Micheli.jpg|thumb|upright=0.7|In 1729, Pier Antonio Micheli first published descriptions of fungi.]]

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.<ref name=Struck2006/>

The use of fungi by humans dates back to prehistory; Ötzi the Iceman, a well-preserved mummy of a 5,300-year-old Neolithic man found frozen in the Austrian Alps, carried two species of polypore mushrooms that may have been used as tinder (''Fomes fomentarius''), or for medicinal purposes (''Piptoporus betulinus'').<ref name=Peintner1998/> 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 crop destruction that was probably caused by pathogenic fungi.{{sfn|Ainsworth|1976|p=1}}

===History=== Mycology became a systematic science after the development of the microscope in the 17th century. Although fungal spores were first observed by Giambattista della Porta in 1588, the seminal work in the development of mycology is considered to be the publication of Pier Antonio Micheli's 1729 work ''Nova plantarum genera''.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=1–2}} Micheli not only observed spores but also showed that, under the proper conditions, they could be induced into growing into the same species of fungi from which they originated.{{sfn|Ainsworth|1976|p=18}} Extending the use of the binomial system of nomenclature introduced by Carl Linnaeus in his ''Species plantarum'' (1753), the Dutch Christiaan Hendrik Persoon (1761–1836) established the first classification of mushrooms with such skill as to be considered a founder of modern mycology. Later, Elias Magnus Fries (1794–1878) further elaborated the classification of fungi, using spore color and microscopic characteristics, methods still used by taxonomists today. Other notable early contributors to mycology in the 17th–19th and early 20th centuries include Miles Joseph Berkeley, August Carl Joseph Corda, Anton de Bary, the brothers Louis René and Charles Tulasne, Arthur H. R. Buller, Curtis G. Lloyd, and Pier Andrea Saccardo. In the 20th and 21st centuries, advances in biochemistry, genetics, molecular biology, biotechnology, DNA sequencing, and phylogenetic analysis have provided new insights into fungal relationships and biodiversity, and have challenged traditional morphology-based groupings in fungal taxonomy.<ref name=Hawksworth2006/>

==Morphology==

===Microscopic structures=== [[File:Penicillium labeled cropped.jpg|thumb|upright=1.5|right|alt=Monochrome micrograph showing ''Penicillium'' hyphae as long, transparent, tube-like structures a few micrometres across. Conidiophores branch out laterally from the hyphae, terminating in bundles of phialides on which spherical condidiophores are arranged like beads on a string. Septa are faintly visible as dark lines crossing the hyphae.|An environmental isolate of ''Penicillium'' {{image key |list type=ordered |Hypha |Conidiophore |Phialide |Conidia |Septa }} ]] Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10{{nbsp}}μm in diameter and up to several centimeters in length. Hyphae grow at their tips (apices); new hyphae are typically formed by emergence of new tips along existing hyphae by a process called ''branching'', or occasionally growing hyphal tips fork, giving rise to two parallel-growing hyphae.<ref name=Harris2008/> Hyphae also sometimes fuse when they come into contact, a process called hyphal fusion (or anastomosis). These growth processes lead to the development of a mycelium, an interconnected network of hyphae.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=30}} 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.{{sfn|Deacon|2005|p=51}} Septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through; an example is the dolipore septum in fungi of the phylum Basidiomycota.{{sfn|Deacon|2005|p=57}} Coenocytic hyphae are in essence multinucleate supercells.<ref name=Chang2004/>

Many species have developed specialized hyphal structures for nutrient uptake from living hosts; examples include haustoria in plant-parasitic species of most fungal phyla,<ref name="Bozkurt et al. 2020"/> and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients.<ref name=Parniske2008/>

Although fungi are opisthokonts—a grouping of evolutionarily related organisms broadly characterized by a single posterior flagellum—all phyla except for the chytrids and blastocladiomycetes have lost their posterior flagella.<ref name=Spatafora2016/><ref name=Steenkamp2006/> 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.<ref name="Gow et al. 2017"/>

===Macroscopic structures=== [[File:Armillaria ostoyae MO.jpg|right|thumb|alt=A cluster of large, thick-stem, light-brown gilled mushrooms growing at the base of a tree|''Armillaria solidipes'']] Fungal mycelia can become visible to the naked eye, for example, on various surfaces and substrates, such as damp walls and spoiled food, where they are commonly called molds. Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as 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.{{sfn|Hanson|2008|pp=127–141}} Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of a clonal colony of ''Armillaria solidipes'', which extends over an area of more than 900{{nbsp}}ha (3.5 square miles), with an estimated age of nearly 9,000{{nbsp}}years.<ref name=Ferguson2003/>

The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped fruit body that is often macroscopic and holds the hymenium, a layer of tissue containing the spore-bearing cells.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=204–205}} The fruit bodies of the basidiomycetes (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well known as mushrooms.

==Growth and physiology== [[File:DecayingPeachSmall.gif|frame|left|alt=Time-lapse photography sequence of a peach becoming progressively discolored and disfigured|Mold growth covering a decaying peach. The frames were taken approximately 12 hours apart over a period of six days.]] The growth of fungi as hyphae on or in solid substrates or as single cells in aquatic environments is adapted for the efficient extraction of nutrients, because these growth forms have high surface area to volume ratios.<ref name=Moss1986/> Hyphae are specifically adapted for growth on solid surfaces, and to invade substrates and tissues.<ref name=Penalva2002/> They can exert large penetrative mechanical forces; for example, many plant pathogens, including ''Magnaporthe grisea'', form a structure called an appressorium that evolved to puncture plant tissues.<ref name=Howard1991/> The pressure generated by the appressorium, directed against the plant epidermis, can exceed {{convert|8|MPa|lk=in}}.<ref name=Howard1991/> The filamentous fungus ''Purpureocillium lilacinum'' uses a similar structure to penetrate the eggs of nematodes.<ref name=Money1997/>

The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol.<ref name=Wang2005/> Adaptations such as these are complemented by hydrolytic enzymes secreted into the environment to digest large organic molecules—such as polysaccharides, proteins, and lipids—into smaller molecules that may then be absorbed as nutrients.<ref name=Pereira2007/><ref name=Schaller2007/><ref name=Farrar1985/> The vast majority of filamentous fungi grow in a polar fashion (extending in one direction) by elongation at the tip (apex) of the hypha.<ref name=Fischer2008/> Other forms of fungal growth include intercalary extension (longitudinal expansion of hyphal compartments that are below the apex) as in the case of some endophytic fungi,<ref name=Christensen2008/> or growth by volume expansion during the development of mushroom stipes and other large organs.<ref name=Money2002/> Growth of fungi as multicellular structures consisting of somatic and reproductive cells—a feature independently evolved in animals and plants<ref name=Willensdorfer2009/>—has several functions, including the development of fruit bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication.<ref name=Daniels2006/>

Fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixed by other organisms for metabolism. Fungi have evolved a high degree of metabolic versatility that allows them to use a diverse range of organic substrates for growth, including simple compounds such as nitrate, ammonia, acetate, or ethanol.<ref name="Tudzynski 2014"/><ref name=Heynes1994/> In some species the pigment melanin may play a role in extracting energy from ionizing radiation, such as gamma radiation. This form of "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlying biophysical and biochemical processes are not well known.<ref name=Dadachova2007/> This process might bear similarity to CO₂ fixation via visible light, but instead uses ionizing radiation as a source of energy.<ref name=Dadachova2008/>

==Reproduction== [[File:Polyporus squamosus Molter.jpg|thumb|right|alt=Two thickly stemmed brownish mushrooms with scales on the upper surface, growing out of a tree trunk|''Cerioporus squamosus'']] Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=48–56}} It is estimated that a third of all fungi reproduce using more than one method of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph (sexual reproduction stage) and the anamorph (asexual reproduction stage).{{sfn|Kirk|Cannon|Minter|Stalpers|2008|p=633}} Environmental conditions trigger genetically determined developmental states that lead to the creation of specialized structures for sexual or asexual reproduction. These structures aid reproduction by efficiently dispersing spores or spore-containing propagules.

===Asexual reproduction=== Asexual reproduction occurs via vegetative spores (conidia) or through mycelial fragmentation. Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each component grows into a separate mycelium. Mycelial fragmentation and vegetative spores maintain clonal populations adapted to a specific niche, and allow more rapid dispersal than sexual reproduction.<ref name=Heitman2005/> The ''Fungi imperfecti'' ('fungi lacking the perfect or sexual stage') or Deuteromycota comprise all the species that lack an observable sexual cycle.<ref name=Alcamo2004/> Deuteromycota (alternatively known as Deuteromycetes, conidial fungi, or mitosporic fungi) is not an accepted taxonomic clade and is now taken to mean simply fungi that lack a known sexual stage.<ref name="Ulloa & Hanlin 2014"/>

===Sexual reproduction=== {{See also|Mating in fungi|Sexual selection in fungi}} Sexual reproduction with meiosis has been directly observed in all fungal phyla except Glomeromycota<ref name=Redecker2006/> (although genetic analysis suggests meiosis occurs in Glomeromycota as well). It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and can be used to discriminate species by morphological differences in sexual structures and reproductive strategies.<ref name=Guarro1999/><ref name=Taylor2000/> Mating experiments between fungal isolates may identify species on the basis of biological species concepts.<ref name=Taylor2000/> 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. Fungi employ two mating systems: heterothallic species allow mating only between individuals of the opposite mating type, whereas homothallic species can mate, and sexually reproduce, with any other individual or itself.<ref name=Metzenberg1990/>

Most fungi have both a haploid and a diploid stage in their life cycles. In sexually reproducing fungi, compatible individuals may combine by fusing their hyphae together into an interconnected network; this process, anastomosis, is required for the initiation of the sexual cycle. Many ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells (see heterokaryosis).{{sfn|Jennings|Lysek|1996|pp=107–114}} [[File:Morelasci.jpg|thumb|left|alt=Microscopic view of numerous translucent or transparent elongated sac-like structures each containing eight spheres lined up in a row|The eight-spore 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'' (crozier) at the hyphal septum. During cell division, the formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (plural ''asci'') is then formed, in which karyogamy (nuclear fusion) occurs. Asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. After dispersal, the ascospores may germinate and form a new haploid mycelium.{{sfn|Deacon|2005|p=31}}

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.{{sfn|Alexopoulos|Mims|Blackwell|1996|pp=492–493}} A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.{{sfn|Jennings|Lysek|1996|p=142}} The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).

In fungi formerly classified as Zygomycota, haploid hyphae of two individuals fuse, forming a gametangium, a specialized cell structure that becomes a fertile gamete-producing cell. The gametangium develops into a zygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which may then form asexual sporangiospores. These sporangiospores allow the fungus to rapidly disperse and germinate into new genetically identical haploid fungal mycelia.{{sfn|Deacon|2005|pp=21–24}}

===Spore dispersal=== The spores of most of the researched species of fungi are transported by wind.<ref name="botany.hawaii">{{cite web |url=http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect05_b.htm |title=Spore Dispersal in Fungi |website=botany.hawaii.edu |access-date=28 December 2018 |archive-url=https://web.archive.org/web/20111117180734/http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect05_b.htm |archive-date=17 November 2011 |url-status=live}}</ref><ref>{{cite web |url=https://herbarium.usu.edu/fun-with-fungi/dispersal |title=Dispersal |website=herbarium.usu.edu |language=en |access-date=28 December 2018 |archive-url=https://web.archive.org/web/20181228223648/https://herbarium.usu.edu/fun-with-fungi/dispersal |archive-date=28 December 2018 |url-status=live}}</ref> Such species often produce dry or hydrophobic spores that do not absorb water and are readily scattered by raindrops, for example.<ref name="botany.hawaii"/><ref>{{cite journal |last1=Hassett |first1=Maribeth O. |last2=Fischer |first2=Mark W. F. |last3=Money |first3=Nicholas P. |title=Mushrooms as Rainmakers: How Spores Act as Nuclei for Raindrops |journal=PLOS ONE |date=28 October 2015 |volume=10 |issue=10 |article-number=e0140407 |doi=10.1371/journal.pone.0140407 |pmid=26509436 |pmc=4624964 |bibcode=2015PLoSO..1040407H |language=en |issn=1932-6203 |doi-access=free |title-link=doi}}</ref><ref>{{cite journal |last1=Kim |first1=Seungho |last2=Park |first2=Hyunggon |last3=Gruszewski |first3=Hope A. |last4=Schmale |first4=David G. |last5=Jung |first5=Sunghwan |title=Vortex-induced dispersal of a plant pathogen by raindrop impact |journal=Proceedings of the National Academy of Sciences |date=12 March 2019 |volume=116 |issue=11 |pages=4917–4922 |doi=10.1073/pnas.1820318116 |pmid=30804195 |pmc=6421443 |bibcode=2019PNAS..116.4917K |language=en |issn=0027-8424 |doi-access=free |title-link=doi}}</ref> In other species, both asexual and sexual spores or sporangiospores are often actively dispersed by forcible ejection from their reproductive structures. This ejection ensures exit of the spores from the reproductive structures as well as traveling through the air over long distances.

[[File:Cyathus stercoreus Fruchtkörper.JPG|thumb|right|alt=A brown, cup-shaped fungus with several greyish disc-shaped structures lying within|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.<ref name=Linder2005/> 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.<ref name=Trail2007/> 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{{nbsp}}g;<ref name=Pringle2005/> the net result is that the spore is ejected 0.01–0.02{{nbsp}}cm, sufficient distance for it to fall through the gills or pores into the air below.{{sfn|Kirk|Cannon|Minter|Stalpers|2008|p=495}} Other fungi, like the puffballs, rely on alternative mechanisms for spore release, such as external mechanical forces. The hydnoid fungi (tooth fungi) produce spores on pendant, tooth-like or spine-like projections.<ref>{{cite web |url=http://www.hampshirebiodiversity.org.uk/pdf/PublishedPlans/ToothFungiSAPfinal.pdf |title=Stipitate hydnoid fungi, Hampshire Biodiversity Partnership |access-date=13 November 2019 |archive-url=https://web.archive.org/web/20160304034104/http://www.hampshirebiodiversity.org.uk/pdf/PublishedPlans/ToothFungiSAPfinal.pdf |archive-date=4 March 2016 |url-status=live}}</ref> The bird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies.<ref name=Brodie1975/> Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=545}}

Some fungi spores are dispersed via animals, for instance truffles and other underground fungi do not actively liberate their spores but instead, most species produce strong-smelling fruitbodies attractive to voles and other small mammals which eat them and disperse the spores in their feces.<ref>{{Cite book |last=Brian Spooner; Peter Roberts |title=Fungi |publisher=HarperCollins Publishers Limited |year=2009 |isbn=9780007308712}}</ref> Likewise insects such as flies and other invertebrates also may disperse spores after ingesting fruiting bodies, or plant matter containing a fungus. Birds have also been known to carry spores of various tree pathogenic fungi.<ref>{{Cite journal |last=Lilleskov |first=Erik A. |last2=Bruns |first2=Thomas D. |date=2005 |title=Spore dispersal of a resupinate ectomycorrhizal fungus, Tomentella sublilacina, via soil food webs |url=https://pubmed.ncbi.nlm.nih.gov/16457345 |journal=Mycologia |volume=97 |issue=4 |pages=762–769 |doi=10.3852/mycologia.97.4.762 |issn=0027-5514 |pmid=16457345}}</ref>

=== Homothallism === In homothallic sexual reproduction, two haploid nuclei derived from the same individual fuse to form a zygote that can then undergo meiosis. Homothallic fungi include species with an ''Aspergillus''-like asexual stage (anamorphs) occurring in numerous different genera,<ref>{{cite journal |author=Dyer PS, O'Gorman CM |title=Sexual development and cryptic sexuality in fungi: insights from ''Aspergillus'' species |date=Jan 2012 |journal=FEMS Microbiology Reviews |volume=36 |issue=1 |pages=165–192 |doi=10.1111/j.1574-6976.2011.00308.x |pmid=22091779 |doi-access=free |title-link=doi |bibcode=2012FEMMR..36..165D }}</ref> several species of the ascomycete genus ''Cochliobolus'',<ref>{{cite journal |vauthors=Yun SH, Berbee ML, Yoder OC, Turgeon BG |year=1999 |title=Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=96 |issue=10 |pages=5592–7 |doi=10.1073/pnas.96.10.5592 |pmid=10318929 |pmc=21905 |bibcode=1999PNAS...96.5592Y |doi-access=free |title-link=doi}}</ref> and the ascomycete ''Pneumocystis jirovecii''.<ref>{{cite journal |vauthors=Richard S, Almeida Jmgcf CO, Luraschi A, Nielsen O, Pagni M, Hauser PM |year=2018 |title=Functional and expression analyses of the ''Pneumocystis'' MAT genes suggest obligate sexuality through primary homothallism within host lungs |journal=mBio |volume=9 |issue=1 |article-number=e02201-17 |doi=10.1128/mBio.02201-17 |doi-access=free|pmid=29463658 |pmc=5821091}}</ref> The earliest mode of sexual reproduction among eukaryotes was likely homothallism, that is, self-fertile unisexual reproduction.<ref name="Heitman 2015">{{cite journal |last1=Heitman |first1=Joseph |title=Evolution of sexual reproduction: A view from the fungal kingdom supports an evolutionary epoch with sex before sexes |journal=Fungal Biology Reviews |volume=29 |issue=3–4 |year=2015 |pages=108–117 |doi=10.1016/j.fbr.2015.08.002 |pmid=26834823 |pmc=4730888 |doi-access=free |title-link=doi |bibcode=2015FunBR..29..108H}}</ref>

===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.{{sfn|Jennings|Lysek|1996|pp=114–115}} 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<ref name=Furlaneto1992/> and is likely required for hybridization between species, which has been associated with major events in fungal evolution.<ref name=Schardl2003/>

==Evolution==

{{Main|Evolution of fungi}}

=== Fossil history ===

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.<ref name=Donoghue2004/> 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.{{sfn|Taylor|Taylor|1993|p=19}} Researchers study compression fossils by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details.{{sfn|Taylor|Taylor|1993|pp=7–12}}

The earliest fossils possessing features typical of fungi date to the Paleoproterozoic era, some {{ma|2400}} (Ma); these multicellular benthic organisms had filamentous structures capable of anastomosis.<ref>{{cite journal |last1=Bengtson |first1=Stefan |last2=Rasmussen |first2=Birger |last3=Ivarsson |first3=Magnus |last4=Muhling |first4=Janet |last5=Broman |first5=Curt |last6=Marone |first6=Federica |last7=Stampanoni |first7=Marco |last8=Bekker |first8=Andrey |s2cid=25586788 |title=Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt |journal=Nature Ecology & Evolution |date=24 April 2017 |volume=1 |issue=6 |page=0141 |doi=10.1038/s41559-017-0141 |pmid=28812648 |bibcode=2017NatEE...1..141B |hdl=20.500.11937/67718 |hdl-access=free |url=https://escholarship.org/uc/item/4883d4qh |access-date=15 July 2019 |archive-url=https://web.archive.org/web/20190715234418/https://escholarship.org/uc/item/4883d4qh |archive-date=15 July 2019 |url-status=live}}</ref> Other studies (2009) estimate the arrival of fungal organisms at about 760–1060{{nbsp}}Ma on the basis of comparisons of the rate of evolution in closely related groups.<ref name=Lucking2009/> The oldest fossilized mycelium to be identified from its molecular composition is between 715 and 810 million years old.<ref>{{Cite web |url=https://phys.org/news/2020-01-mushrooms-earlier-previously-thought.html |title=First mushrooms appeared earlier than previously thought |access-date=14 October 2023 |archive-date=27 October 2023 |archive-url=https://web.archive.org/web/20231027061656/https://phys.org/news/2020-01-mushrooms-earlier-previously-thought.html |url-status=live }}</ref> For much of the Paleozoic Era (542–251{{nbsp}}Ma), the fungi appear to have been aquatic and consisted of organisms similar to the extant chytrids in having flagellum-bearing spores.<ref name=James2006b/> 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.{{sfn|Taylor|Taylor|1993|pp=84–94 & 106–107}} Studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.<ref name=Schoch2009/>

In May 2019, scientists reported the discovery of a fossilized fungus, named ''Ourasphaira giraldae'', in the Canadian Arctic, that may have grown on land a billion years ago, well before plants were living on land.<ref name="NYT-20190522">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=How Did Life Arrive on Land? A Billion-Year-Old Fungus May Hold Clues – A cache of microscopic fossils from the Arctic hints that fungi reached land long before plants. |date=22 May 2019 |work=The New York Times |url=https://www.nytimes.com/2019/05/22/science/fungi-fossils-plants.html |access-date=23 May 2019 |archive-url=https://web.archive.org/web/20190523011853/https://www.nytimes.com/2019/05/22/science/fungi-fossils-plants.html |archive-date=23 May 2019 |url-status=live}}</ref><ref name="NAT-20190522">{{cite journal |last1=Loron |first1=Corentin C. |last2=François |first2=Camille |last3=Rainbird |first3=Robert H. |last4=Turner |first4=Elizabeth C. |last5=Borensztajn |first5=Stephan |last6=Javaux |first6=Emmanuelle J. |s2cid=162180486 |title=Early fungi from the Proterozoic era in Arctic Canada |journal=Nature |volume=570 |issue=7760 |pages=232–235 |publisher=Springer Science and Business Media LLC |date=22 May 2019 |issn=0028-0836 |doi=10.1038/s41586-019-1217-0 |pmid=31118507 |bibcode=2019Natur.570..232L |url=https://insu.hal.science/insu-03586648 }}</ref><ref name="Ars Technica 2019">{{cite web |last=Timmer |first=John |title=Billion-year-old fossils may be early fungus |website=Ars Technica |date=22 May 2019 |url=https://arstechnica.com/science/2019/05/billion-year-old-fossils-may-be-early-fungus/ |access-date=23 May 2019 |archive-url=https://web.archive.org/web/20190523003551/https://arstechnica.com/science/2019/05/billion-year-old-fossils-may-be-early-fungus/ |archive-date=23 May 2019 |url-status=live}}</ref> Pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) have been reported in South China.<ref>{{cite journal |last1=Gan |first1=Tian |last2=Luo |first2=Taiyi |last3=Pang |first3=Ke |last4=Zhou |first4=Chuanming |last5=Zhou |first5=Guanghong |last6=Wan |first6=Bin |last7=Li |first7=Gang |last8=Yi |first8=Qiru |last9=Czaja |first9=Andrew D. |last10=Xiao |first10=Shuhai |title=Cryptic terrestrial fungus-like fossils of the early Ediacaran Period |date=28 January 2021 |journal=Nature Communications |language=en |volume=12 |issue=1 |page=641 |doi=10.1038/s41467-021-20975-1 |pmid=33510166 |pmc=7843733 |bibcode=2021NatCo..12..641G |issn=2041-1723 |doi-access=free |title-link=doi}}</ref> Earlier, it had been presumed that the fungi colonized the land during the Cambrian (542–488.3{{nbsp}}Ma), also long before land plants.<ref name=Brundrett2002/> Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460{{nbsp}}Ma) resemble modern-day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like plants.<ref name=Redecker2000/> ''Prototaxites'', which was possibly a fungus or lichen, would have been the tallest organism of the late Silurian and early Devonian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–359.2{{nbsp}}Ma), when they occur abundantly in the Rhynie chert, mostly as Zygomycota and Chytridiomycota.<ref name=Brundrett2002/><ref name=Taylor1996/><ref name=Dotzler2009/> At about this same time, approximately 400{{nbsp}}Ma, the Ascomycota and Basidiomycota diverged,<ref name=Taylor2006/> and all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299{{nbsp}}Ma).<ref name="urlFungi"/>

Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 415{{nbsp}}Ma;<ref name="Honegger et al. 2013"/> this date roughly corresponds to the age of the oldest known sporocarp fossil, a ''Paleopyrenomycites'' species found in the Rhynie Chert.<ref name=Taylor2005/> The oldest fossil with microscopic features resembling modern-day basidiomycetes is ''Palaeoancistrus'', found permineralized with a fern from the Pennsylvanian.<ref name=Dennis1970/> Rare in the fossil record are the Homobasidiomycetes (a taxon roughly equivalent to the mushroom-producing species of the Agaricomycetes). Two amber-preserved specimens provide evidence that the earliest known mushroom-forming fungi (the extinct species ''Archaeomarasmius leggetti'') appeared during the late Cretaceous, 90{{nbsp}}Ma.<ref name=Hibbett1995/><ref name=Hibbett1997/>

Some time after the Permian–Triassic extinction event (251.4{{nbsp}}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.<ref name=Eshet1995/> However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess,<ref name=Foster2002/> the spike did not appear worldwide,<ref name=LopezGomez2005/><ref name=Looy2005/> and in many places it did not fall on the Permian–Triassic boundary.<ref name=Ward2005/>

Sixty-five million years ago, immediately after the Cretaceous–Paleogene extinction event that famously killed off most dinosaurs, there was a dramatic increase in evidence of fungi; apparently the death of most plant and animal species led to a huge fungal bloom like "a massive compost heap".<ref>{{cite journal |last1=Casadevall |first1=Arturo |last2=Heitman |first2=Joseph |title=Fungi and the Rise of Mammals |journal=PLOS Pathogens |date=16 August 2012 |volume=8 |issue=8 |article-number=e1002808 |doi=10.1371/journal.ppat.1002808 |pmid=22916007 |pmc=3420938 |quote=That ecological calamity was accompanied by massive deforestation, an event followed by a fungal bloom, as the earth became a massive compost. |doi-access=free |title-link=doi}}</ref>

=== External phylogeny ===

Although commonly included in botany curricula and textbooks, fungi are more closely related to animals than to plants, and are placed with the animals in the monophyletic group of opisthokonts.<ref name=ShalchianTabrizi2008/> Analyses using molecular phylogenetics support a monophyletic origin of fungi.<ref name=Hibbett2007/><ref name="Li et al 2021"/> The taxonomy of fungi is in a state of constant flux, especially due to 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.<ref>{{cite web |url=http://palaeos.com/fungi/fungi.html |title=Palaeos Fungi: Fungi |archive-url=https://web.archive.org/web/20120620205340/http://palaeos.com/fungi/fungi.html |archive-date=20 June 2012}} for an introduction to fungal taxonomy, including controversies. [https://web.archive.org/web/20041114121617/http://www.palaeos.com/Fungi/default.htm archive]</ref>

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.<ref name=Hibbett2007/><ref name=Celio2006/> Until relatively recent (2012) changes to the International Code of Nomenclature for algae, fungi and plants, fungal species could also have multiple scientific names depending on their life cycle and mode (sexual or asexual) of reproduction.<ref name="Rossman 2014"/> Web sites such as Index Fungorum, Fungal Names, and MycoBank are officially recognized nomenclatural repositories and list current names of fungal species (with cross-references to older synonyms).<ref name="Redhead & Norvell 2013"/>

=== Internal phylogeny ===

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.<ref name=Hibbett2007/> It recognizes seven phyla, two of which—the Ascomycota and the Basidiomycota—are contained within a branch representing subkingdom Dikarya, the most species rich and familiar group, including all the mushrooms, most food-spoilage molds, most plant pathogenic fungi, and the beer, wine, and bread yeasts. The accompanying cladogram depicts the major fungal taxa and their relationship to opisthokont and unikont organisms, based on the work of Philippe Silar,<ref name=Silar2016/> "The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research"<ref name=MycotaVIIS&E/> and Tedersoo et al. 2018.<ref name=Tedersoo>{{cite journal |last1=Tedersoo |first1=Leho |last2=Sanchez-Ramırez |first2=Santiago |last3=Koljalg |first3=Urmas |last4=Bahram |first4=Mohammad |last5=Doring |first5=Markus |last6=Schigel |first6=Dmitry |last7=May |first7=Tom |last8=Ryberg |first8=Martin |last9=Abarenkov |first9=Kessy |title=High-level classification of the Fungi and a tool for evolutionary ecological analyses |journal=Fungal Diversity |date=22 February 2018 |volume=90 |issue=1 |pages=135–159 |doi=10.1007/s13225-018-0401-0 |doi-access=free |title-link=doi|hdl=10138/238983 |hdl-access=free }}</ref> The lengths of the branches are not proportional to evolutionary distances.

{{Clade |style=font-size:100%; line-height:80% |label1=Zoosporia |1={{clade |1={{clade <!-- dummy clade to reduce horizontal width --> |label1=Rozellomyceta |1={{clade |label1=Rozellomycota |1=Rozellomycetes |label2=Microsporidiomycota |2={{clade |1=''Mitosporidium'' |2={{clade |1=''Paramicrosporidium'' |2={{clade |1=''Nucleophaga'' |2={{clade |1=Metchnikovellea |2=Microsporea }} }} }} }} }} }} |2={{clade |label1=Aphelidiomyceta |1={{clade |label1=Aphelidiomycota |1=Aphelidiomycetes }} |label2=Eumycota{{efn|name=eumycota}} |2={{clade |1={{clade <!-- dummy clade to reduce horizontal width --> |label1=Chytridiomyceta |1={{clade |label1=Neocallimastigomycota |1=Neocallimastigomycetes |label2=Chytridiomycota |2={{clade |label1=Monoblepharomycotina |1={{clade |1=Hyaloraphidiomycetes |3=Sanchytriomycetes |2=Monoblepharidomycetes }} |label2=Chytridiomycotina |2={{clade |1=Mesochytriomycetes |2=Chytridiomycetes }} }} }} }} |2={{clade |label1=Blastocladiomyceta |label2=Amastigomycota |1={{clade |label1=Blastocladiomycota |1={{clade |1=Blastocladiomycetes |2=Physodermatomycetes }} }} |2={{clade |1={{clade <!-- dummy clade to reduce horizontal width --> |label1=Zoopagomyceta |1={{clade |1={{clade |1=Basidiobolomyceta |2=Olpidiomyceta }} |2={{clade |label1=Entomophthoromycota |1={{clade |1=Neozygitomycetes |2=Entomophthoromycetes }} |label2=Kickxellomycota |2={{clade |label1=Zoopagomycotina |1=Zoopagomycetes |label2=Kickxellomycotina |2={{clade |1=Dimargaritomycetes |2=Kickxellomycetes }} }} }} }} }} |2={{clade |1={{clade <!-- dummy clade to reduce horizontal width --> |label1=Mortierellomycota |1=Mortierellomycetes }} |2={{clade |label1=Mucoromyceta{{efn|In protein-based analyses, Mucoromyceta is a clade that also includes Mortierellomycota and Glomeromycota.<ref name=Tedersoo/>}} |1={{clade |label1=Calcarisporiellomycota |1=Calcarisporiellomycetes |label2=Mucoromycota |2={{clade |1=Umbelopsidomycetes |2=Mucoromycetes }} }} |label2=Symbiomycota |2={{clade |label1=Glomeromycota |1={{clade |1=Paraglomeromycetes |2={{clade |1=Archaeosporomycetes |2=Glomeromycetes }} }} |label2=Dikarya |2={{clade |1={{clade |label1=Entorrhizomycota |1=Entorrhizomycetes |2=Basidiomycota }} |2=Ascomycota }} }} }} }} }} }} }} }} }} }}

{{Clade |style=font-size:100%; line-height:80% |label1=Basidiomycota |1={{clade |label1=Pucciniomycotina |1={{clade |1={{clade |1=Tritirachiomycetes |2={{clade |1=Mixiomycetes |2=Agaricostilbomycetes }} }} |2={{clade |1=Cystobasidiomycetes |2={{clade |1={{clade |1=Classiculaceae |2=Microbotryomycetes }} |2={{clade |1=Cryptomycocolacomycetes |2={{clade |1=Atractiellomycetes |2=Pucciniomycetes }} }} }} }} }} |label2=Orthomycotina |2={{clade |label1=Ustilaginomycotina |1={{clade |1={{clade |1=Monilielliomycetes |2=Malasseziomycetes }} |2={{clade |1=Ustilaginomycetes |2=Exobasidiomycetes }} }} |label2=Agaricomycotina |2={{clade |1=?Geminibasidiomycetes |2=?Wallemiomycetes |3=Bartheletiomycetes |4={{clade |1=Tremellomycetes |2={{clade |1=Dacrymycetes |2=Agaricomycetes }} }} }} }} }} }}

{{Clade |style=font-size:100%; line-height:80% |label1=Ascomycota |1={{clade |label1=Taphrinomycotina |1={{clade |1={{clade |1=Neolectomycetes |2=Taphrinomycetes }} |label2=Schizosaccharomyceta |2={{clade |1=Archaeorhizomycetes |2={{clade |1=Pneumocystidomycetes |2=Schizosaccharomycetes }} }} }} |label2=Saccharomyceta |2={{clade |label1=Saccharomycotina |1=Saccharomycetes |label2=Pezizomycotina |2={{clade |1=?Thelocarpales |2=?Vezdaeales |3=?Lahmiales |4=?Triblidiales |5=Orbiliomycetes |6={{clade |1=Pezizomycetes |label2=Leotiomyceta |2={{clade |label1=Sordariomyceta |1={{clade |1=Xylonomycetes |2={{clade |1=Geoglossomycetes |2={{clade |1=Leotiomycetes |2={{clade |1=Laboulbeniomycetes |2=Sordariomycetes }} }} }} }} |label2=Dothideomyceta |2={{clade |1={{clade |1=Coniocybomycetes |2=Lichinomycetes }} |2={{clade |1={{clade |1=Eurotiomycetes |2=Lecanoromycetes }} |2={{clade |1=Collemopsidiomycetes |2={{clade |1=Arthoniomycetes |2=Dothideomycetes }} }} }} }} }} }} }} }} }} }}

===Taxonomic groups=== {{See also|List of fungal orders}} thumb|right|upright=1.5|Main groups of fungi The major phyla (sometimes called divisions) of fungi have been classified mainly on the basis of characteristics of their sexual reproductive structures. {{As of|2019}}, nine major lineages have been identified: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycotina, Mucoromycota, Glomeromycota, Ascomycota, and Basidiomycota.<ref name="Naranjo‐Ortiz & Gabaldón 2019"/>

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).<ref name=James2006b/> Previously considered to be "primitive" protozoa, they are now thought to be either a basal branch of the Fungi, or a sister group–each other's closest evolutionary relative.<ref name="Han et al. 2017"/>

The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide. Chytrids and their close relatives Neocallimastigomycota and Blastocladiomycota (below) are the only fungi with active motility, producing zoospores that are capable of active movement through aqueous phases with a single flagellum, leading early taxonomists to classify them as protists. Molecular 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.<ref name=James2006/>

The Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. 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, most of which exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis.<ref name=James2006b/>

The Neocallimastigomycota were earlier placed in the phylum Chytridiomycota. Members of this small phylum are anaerobic organisms, living in the digestive system of larger herbivorous mammals and in other terrestrial and aquatic environments enriched in cellulose (e.g., domestic waste landfill sites).<ref name=Lockhart2006/> They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As in the related chytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.<ref name=Hibbett2007/>

[[File:Arbuscular mycorrhiza microscope.jpg|thumb|right|alt=Microscopic view of a layer of translucent grayish cells, some containing small dark-color spheres|''Arbuscular mycorrhiza'' seen under microscope. Flax root cortical cells containing paired arbuscules.]] [[File:Ascocarp2.png|thumb|right|alt=Cross-section of a cup-shaped structure showing locations of developing meiotic asci (upper edge of cup, left side, arrows pointing to two gray cells containing four and two small circles), sterile hyphae (upper edge of cup, right side, arrows pointing to white cells with a single small circle in them), and mature asci (upper edge of cup, pointing to two gray cells with eight small circles in them)|Diagram of an apothecium (the typical cup-like reproductive structure of ascomycetes) showing sterile tissues as well as developing and mature asci]] Members of the Glomeromycota form arbuscular mycorrhizae, a form of mutualist symbiosis wherein fungal hyphae invade plant root cells and both species benefit from the resulting increased supply of nutrients. All known Glomeromycota species reproduce asexually.<ref name=Redecker2006/> The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400&nbsp;million years ago.<ref name=Remy1994/> 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.<ref name=Schussler2001/> 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.<ref name=Hibbett2007/> 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.{{sfn|Alexopoulos|Mims|Blackwell|1996|p=145}} Medically relevant genera include ''Mucor'', ''Rhizomucor'', and ''Rhizopus''.<ref name="Walther et al. 2019"/>

The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota.{{sfn|Kirk|Cannon|Minter|Stalpers|2008|p=489}} 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, unicellular yeasts (e.g., of the genera ''Saccharomyces'', ''Kluyveromyces'', ''Pichia'', and ''Candida''), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes include ''Aspergillus'', ''Penicillium'', ''Fusarium'', and ''Claviceps''. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), but analysis of molecular data has often been able to identify their closest teleomorphs in the Ascomycota.<ref name=Samuels2006/> 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'').<ref name="Aramayo et al. 2013"/>

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'',<ref name="Olicón-Hernández et al. 2019"/> human commensal species of the genus ''Malassezia'',<ref name="Rhimi et al. 2020"/> and the opportunistic human pathogen, ''Cryptococcus neoformans''.<ref name=Perfect2006/>

===Fungus-like organisms=== Because of similarities in morphology and lifestyle, the slime molds (mycetozoans, plasmodiophorids, acrasids, ''Fonticula'', and labyrinthulids, now in Amoebozoa, Rhizaria, Excavata, Cristidiscoidea, and Stramenopiles, respectively), water molds (oomycetes) and hyphochytrids (both Stramenopiles) were formerly classified in the kingdom Fungi, in groups like Mastigomycotina, Gymnomycota and Phycomycetes. The slime molds were studied also as protozoans, leading to an ambiregnal, duplicated taxonomy.<ref name="Leontyev & Schnittler 2017"/>

Unlike true fungi, the cell walls of oomycetes contain cellulose and lack chitin. Hyphochytrids have both chitin and cellulose. Slime molds lack a cell wall during the assimilative phase (except labyrinthulids, which have a wall of scales), and take in nutrients by ingestion (phagocytosis, except labyrinthulids) rather than absorption (osmotrophy, as fungi, labyrinthulids, oomycetes and hyphochytrids). Neither water molds nor slime molds are closely related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in mycology textbooks and primary research literature.<ref name=Blackwell2004/>

The Eccrinales and Amoebidiales are opisthokont protists, previously thought to be zygomycete fungi. Other groups now in Opisthokonta (e.g., ''Corallochytrium'', Ichthyosporea) were also at given time classified as fungi. The genus ''Blastocystis'', now in Stramenopiles, was originally classified as a yeast. ''Ellobiopsis'', now in Alveolata, was considered a chytrid. The bacteria were also included in fungi in some classifications, as the group Schizomycetes.

The Rozellida clade, including the "ex-chytrid" ''Rozella'', is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi.<ref name="Naranjo‐Ortiz & Gabaldón 2019"/> Members of the group that have been isolated lack the chitinous cell wall that is characteristic of fungi. Alternatively, Rozella can be classified as a basal fungal group.<ref name="Li et al 2021"/>

The nucleariids may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom.<ref name="ShalchianTabrizi2008"/> Many Actinomycetales (Actinomycetota), a group with many filamentous bacteria, were also long believed to be fungi.<ref>{{cite book |last1=Amoroso |first1=Maria Julia |last2=Benimeli |first2=Claudia Susana |last3=Cuozzo |first3=Sergio Antonio |title=Actinobacteria: application in bioremediation and production of industrial enzymes |date=2013 |publisher=CRC Press, Taylor & Francis Group |isbn=978-1-4665-7873-9 |page=33 |url=https://www.crcpress.com/Actinobacteria-Application-in-Bioremediation-and-Production-of-Industrial/Amoroso-Benimeli-Cuozzo/p/book/9781466578739 |language=en}}</ref><ref>{{cite web |url=https://www.humankindoregon.com/soil-biology |title=An Introduction to Soil Biology |website=Humankind Oregon |access-date=13 November 2019 |archive-date=31 July 2020 |archive-url=https://web.archive.org/web/20200731225405/https://www.humankindoregon.com/soil-biology |url-status=live }}</ref>

==Ecology== thumb|A pin mold decomposing a peach 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 aquatic ecosystems, and therefore play a critical role in biogeochemical cycles<ref name=Gadd2007/> 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.<ref name=Lindahl2007/><ref name=Barea2005/>

===Symbiosis=== Many fungi have important symbiotic relationships with organisms from most if not all kingdoms.<ref name=Aanen2006/><ref name=Nikoh2000/><ref name=Perotto1997/> 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.<ref name=Arnold2003/><ref name=Paszkowski2006/><ref name=Hube2004/>

====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.<ref name=Bonfante2003/> [[File:Neotyphodium coenophialum.jpg|thumb|left|upright=0.75|alt=A microscopic view of blue-stained cells, some with dark wavy lines in them|The dark filaments are hyphae of the endophytic fungus ''Epichloë coenophiala'' in the intercellular spaces of tall fescue leaf sheath tissue]] The mycorrhizal symbiosis is ancient, dating back to at least 400&nbsp;million years.<ref name=Remy1994/> 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.<ref name=Lindahl2007/><ref name=Heijden2006/> The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients.<ref>{{cite journal |last=Heijden |first=Marcel G. A. van der |s2cid=133399719 |title=Underground networking |date=15 April 2016 |journal=Science |language=en |volume=352 |issue=6283 |pages=290–291 |doi=10.1126/science.aaf4694 |issn=0036-8075 |pmid=27081054 |bibcode=2016Sci...352..290H |hdl=1874/344517 |hdl-access=free}}</ref> Such mycorrhizal communities are called "common mycorrhizal networks".<ref name=Selosse2006/><ref>{{cite web |url=https://www.theatlantic.com/science/archive/2016/04/the-wood-wide-web/478224/ |title=Trees Have Their Own Internet |last=Yong |first=Ed |date=14 April 2016 |website=The Atlantic |language=en-US |access-date=9 March 2019 |archive-url=https://web.archive.org/web/20190328164827/https://www.theatlantic.com/science/archive/2016/04/the-wood-wide-web/478224/ |archive-date=28 March 2019 |url-status=live}}</ref> A special case of mycorrhiza is myco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont.<ref name=Merckx2009/> Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.<ref name=Schulz2005/> 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.<ref name=Clay2002/>

====With algae and cyanobacteria==== [[File:Lobaria pulmonaria 010108a.jpg|right|thumb|alt=A green, leaf-like structure attached to a tree, with a pattern of ridges and depression on the bottom surface|The lichen ''Lobaria pulmonaria'', a symbiosis of fungal, algal, and cyanobacterial species]] Lichens are a symbiotic relationship between fungi and photosynthetic algae or cyanobacteria. The photosynthetic partner in the relationship is referred to in lichen terminology as a "photobiont". The fungal part of the relationship is composed mostly of various species of ascomycetes and a few basidiomycetes.<ref name=Brodo2001/> Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession,<ref name=Raven2005/> and are prominent in some extreme environments, including polar, alpine, and semiarid desert regions.{{sfn|Deacon|2005|p=267}} They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves.<ref name=Purvis2000/> As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis to the fungus, while the fungus provides minerals and water to the photobiont. The functions of both symbiotic organisms are so closely intertwined that they function almost as a single organism; in most cases the resulting organism differs greatly from the individual components.{{sfn|Kirk|Cannon|Minter|Stalpers|2008|p=378}} Lichenization is a common mode of nutrition for fungi; around 27% of known fungi—more than 19,400 species—are lichenized.<ref name="Garrido-Benavent & Pérez-Ortega 2017"/> 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.{{sfn|Deacon|2005|pp=267–276}}

====With insects==== Many insects also engage in mutualistic relationships with fungi. Several groups of ants cultivate fungi in the order Chaetothyriales for several purposes: as a food source, as a structural component of their nests, and as a part of an ant/plant symbiosis in the domatia (tiny chambers in plants that house arthropods).<ref name="Chomicki & Renner 2017"/> Ambrosia beetles cultivate various species of fungi in the bark of trees that they infest.<ref name="Joseph & Keyhani 2021"/> Likewise, 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.{{sfn|Deacon|2005|p=277}} At least one species of stingless bee has a relationship with a fungus in the genus ''Monascus'', where the larvae consume and depend on fungus transferred from old to new nests.<ref name=Sci-News2015/> Termites on the African savannah are also known to cultivate fungi,<ref name=Aanen2006/> 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.<ref name=Nguyen2007/> Fungi growing in dead wood are essential for xylophagous insects (e.g. woodboring beetles).<ref name="Nutritional dynamics">{{cite journal |last1=Filipiak |first1=Michał |last2=Weiner |first2=January |title=Nutritional dynamics during the development of xylophagous beetles related to changes in the stoichiometry of 11 elements |date=March 2017 |journal=Physiological Entomology |volume=42 |issue=1 |pages=73–84 |doi=10.1111/phen.12168 |doi-access=free |title-link=doi |bibcode=2017PhysE..42...73F }}</ref><ref name="Ulyshen page 429-469">{{cite book |last1=Ulyshen |first1=Michael D. |title=Saproxylic Insects |chapter=Nutrient Dynamics in Decomposing Dead Wood in the Context of Wood Eater Requirements: The Ecological Stoichiometry of Saproxylophagous Insects |series=Zoological Monographs |date=2018 |volume=1 |publisher=Springer, Cham |isbn=978-3-319-75937-1 |pages=429–469 |doi=10.1007/978-3-319-75937-1_13 |url=https://depot.ceon.pl/handle/123456789/15394?show=full}}</ref><ref name="Ulyshen page 377-427">{{cite book |last1=Ulyshen |first1=Michael D. |title=Saproxylic Insects |chapter=Insect-Fungus Interactions in Dead Wood Systems |series=Zoological Monographs |date=2018 |volume=1 |publisher=Springer, Cham |isbn=978-3-319-75936-4 |pages=377–427 |doi=10.1007/978-3-319-75937-1_12}}</ref> They deliver nutrients needed by xylophages to nutritionally scarce dead wood.<ref>{{cite journal |last1=Filipiak |first1=Michał |last2=Sobczyk |first2=Łukasz |last3=Weiner |first3=January |year=2016 |title=Fungal transformation of tree stumps into a suitable resource for xylophagous beetles via changes in elemental ratios |journal=Insects |volume=7 |issue=2 |page=13 |doi=10.3390/insects7020013 |pmc=4931425 |doi-access=free |title-link=doi}}</ref><ref name="Ulyshen page 429-469"/><ref name="Ulyshen page 377-427"/> Thanks to this nutritional enrichment the larvae of the woodboring insect is able to grow and develop to adulthood.<ref name="Nutritional dynamics"/> The larvae of many families of fungicolous flies, particularly those within the superfamily Sciaroidea such as the Mycetophilidae and some Keroplatidae feed on fungal fruiting bodies and sterile mycorrhizae.<ref name="Jakovlev 2012"/>

====As parasites==== {{anchor|Parasite|Pathogen|Necrotroph}}

[[File:Ophiocordyceps unilateralis - Denis Zabin - 407452035.jpeg|thumb|Zombie ants, infected by the ''Ophiocordyceps unilateralis'' fungus, are predominantly found in tropical rainforests.]] 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'',<ref name="Fernandez & Orth 2018"/> tree pathogens such as ''Ophiostoma ulmi'' and ''Ophiostoma novo-ulmi'' causing Dutch elm disease,<ref name="Santini & Battisti 2019"/> ''Cryphonectria parasitica'' responsible for chestnut blight,<ref name="Rigling & Prospero 2018"/> and ''Phymatotrichopsis omnivora'' causing Texas root rot, and plant pathogens in the genera ''Fusarium'', ''Ustilago'', ''Alternaria'', and ''Cochliobolus''.<ref name=Paszkowski2006/> Some carnivorous fungi, like ''Purpureocillium lilacinum'', are predators of nematodes, which they capture using an array of specialized structures such as constricting rings or adhesive nets.<ref name=Yang2007/> Many fungi that are plant pathogens, such as ''Magnaporthe oryzae'', can switch from being biotrophic (parasitic on living plants) to being necrotrophic (feeding on the dead tissues of plants they have killed).<ref>{{cite journal |last1=Koeck |first1=M. |last2=Hardham |first2=A.R. |last3=Dodds |last4=P.N. |date=2011 |volume=13 |issue=12 |pages=1849–1857 |title=The role of effectors of biotrophic and hemibiotrophic fungi in infection |journal=Cellular Microbiology |doi=10.1111/j.1462-5822.2011.01665.x |pmid=21848815 |pmc=3218205}}</ref> This same principle is applied to fungi-feeding parasites, including ''Asterotremella albida'', which feeds on the fruit bodies of other fungi both while they are living and after they are dead.<ref>{{cite web |url=https://www.researchgate.net/publication/6114636 |title=''Asterotremella gen. nov. albida'', an anamorphic tremelloid yeast isolated from the agarics ''Asterophora lycoperdoides'' and ''Asterophora parasitica'' |via=ResearchGate |language=en |access-date=19 April 2019}}</ref>

Some fungi alter the behavior of their animal hosts in ways that spread their spores more effectively (also called "active host transmission"). Examples include ''Ophiocordyceps unilateralis'' and possibly the extinct ''Allocordyceps''.

====As pathogens==== [[File:Aecidium magnellanicum.jpg|right|thumb|alt=A thin brown stick positioned horizontally with roughly two dozen clustered orange-red leaves originating from a single point in the middle of the stick. These orange leaves are three to four times larger than the few other green leaves growing out of the stick, and are covered on the lower leaf surface with hundreds of tiny bumps. The background shows the green leaves and branches of neighboring shrubs.|The plant pathogen ''Puccinia magellanicum'' (calafate rust) causes the defect known as witch's broom, seen here on a barberry shrub in Chile.]] [[File:Candida Gram stain.jpg|thumb|right|Gram stain of ''Candida albicans'' from a vaginal swab from a woman with candidiasis, showing hyphae, and chlamydospores, which are 2–4 μm in diameter]]

Some fungi can cause serious diseases in humans, several of which may be fatal if untreated. These include aspergillosis, candidiasis, coccidioidomycosis, cryptococcosis, histoplasmosis, mycetomas, and paracoccidioidomycosis. Furthermore, a person with immunodeficiency is more susceptible to disease by genera such as ''Aspergillus'', ''Candida'', ''Cryptoccocus'',<ref name=Hube2004/><ref name=Nielsen2007/><ref name=Brakhage2005/> ''Histoplasma'',<ref name=Kauffman2007/> and ''Pneumocystis''.<ref name=Cushion2007/> 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.<ref name=Cook2008/> Fungal spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic reactions.<ref name=SimonNobbe2008/>

====As targets of mycoparasites==== Organisms that parasitize fungi are known as mycoparasitic organisms. About 300 species of fungi and fungus-like organisms, belonging to 13 classes and 113 genera, are used as biocontrol agents against plant fungal diseases.<ref name="Thambugala et al. 2020"/> Fungi can also act as mycoparasites or antagonists of other fungi, such as ''Hypomyces chrysospermus'', which grows on bolete mushrooms. Fungi can also become the target of infection by mycoviruses.<ref name="Pearson">{{cite journal |vauthors=Pearson MN, Beever RE, Boine B, Arthur K |title=Mycoviruses of filamentous fungi and their relevance to plant pathology |journal=Molecular Plant Pathology |volume=10 |issue=1 |pages=115–28 |date=January 2009 |pmid=19161358 |doi=10.1111/j.1364-3703.2008.00503.x |pmc=6640375|bibcode=2009MolPP..10..115P }}</ref><ref name="Boz">{{cite journal |vauthors=Bozarth RF |title=Mycoviruses: a new dimension in microbiology |journal=Environmental Health Perspectives |volume=2 |issue=1 |pages=23–39 |date=October 1972 |pmid=4628853 |pmc=1474899 |doi=10.1289/ehp.720223|bibcode=1972EnvHP...2...23B }}</ref>

===Communication=== {{Main|Mycorrhizal networks}}

There appears to be electrical communication between fungi in word-like components according to spiking characteristics.<!--The spiking characteristics were specific to the fungi species and were often clustered into sentence-like series. The study found that size of fungal lexicon can be up to 50 words in the four investigated species while the most frequently used ones do not exceed 15–20 words. However, the meaning or informational content, if there is any, remains unknown.<ref>{{cite news |title=Mushrooms communicate with each other using up to 50 'words', scientist claims |url=https://www.theguardian.com/science/2022/apr/06/fungi-electrical-impulses-human-language-study |access-date=13 May 2022 |work=The Guardian |date=5 April 2022 |language=en}}</ref><ref>{{cite news |last1=Field |first1=Katie |title=Do mushrooms really use language to talk to each other? A fungi expert investigates |url=https://phys.org/news/2022-04-mushrooms-language-fungi-expert.html |access-date=13 May 2022 |work=The Conversation |language=en}}</ref>--><ref>{{cite journal |last1=Adamatzky |first1=Andrew |title=Language of fungi derived from their electrical spiking activity |journal=Royal Society Open Science |year=2022 |volume=9 |issue=4 |article-number=211926 |doi=10.1098/rsos.211926 |doi-access=free|pmid=35425630 |pmc=8984380 |arxiv=2112.09907 |bibcode=2022RSOS....911926A}}</ref>

===Possible impact on climate=== According to a study published in the academic journal Current Biology, fungi can soak from the atmosphere around 36% of global fossil fuel greenhouse gas emissions.<ref>{{cite news |last1=ELBEIN |first1=SAUL |title=Fungi may offer 'jaw-dropping' solution to climate change |url=https://thehill.com/policy/equilibrium-sustainability/4034986-fungi-may-offer-jaw-dropping-solution-to-climate-change/ |access-date=6 June 2023 |agency=The Hill |date=6 June 2023 |archive-date=6 June 2023 |archive-url=https://web.archive.org/web/20230606030741/https://thehill.com/policy/equilibrium-sustainability/4034986-fungi-may-offer-jaw-dropping-solution-to-climate-change/ |url-status=live }}</ref><ref>{{cite web |title=Fungi stores a third of carbon from fossil fuel emissions and could be essential to reaching net zero, new study reveals |url=https://www.eurekalert.org/news-releases/991288 |website=EurekAlert |publisher=UNIVERSITY OF SHEFFIELD |access-date=6 June 2023 |archive-date=6 June 2023 |archive-url=https://web.archive.org/web/20230606010252/https://www.eurekalert.org/news-releases/991288 |url-status=live }}</ref> This is because mycorrhizal fungi that directly participate in photosynthesis create a network that holds the soil together at the same time. Such fungi are severely threatened by herbicides, fungicides, fertlizers, deforestation, pollution and covering soil with impermeable materials like concrete.<ref name=Paul>{{cite web |last1=Tullis |first1=Paul |title=The underground network |url=https://thebulletin.org/2026/01/the-underground-network-prehistoric-fungi-feed-the-worlds-plants-and-resist-climate-change-but-face-an-uncertain-future/ |website=Bulletin of Atomic scientists |access-date=30 January 2026}}</ref>

==Mycotoxins== [[File:Ergotamine3.png|thumb|right|alt=(6aR,9R)-N-((2R,5S,10aS,10bS)-5-benzyl-10b-hydroxy-2-methyl-3,6-dioxooctahydro-2H-oxazolo[3,2-a] pyrrolo[2,1-c]pyrazin-2-yl)-7-methyl-4,6,6a,7,8,9-hexahydroindolo[4,3-fg] quinoline-9-carboxamide|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''.<ref name=Schardl2007/> 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.<ref name="Janik et al. 2020"/>

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.<ref name=Keller2005/> Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory).<ref name=Demain2000/><ref name=Rohlfs2007/> Many fungal secondary metabolites (or derivatives) are used medically, as described under Human use below.

==Pathogenic mechanisms== ''Ustilago maydis'' is a pathogenic plant fungus that causes smut disease in maize and teosinte. Plants have evolved efficient defense systems against pathogenic microbes such as ''U. maydis''. A rapid defense reaction after pathogen attack is the oxidative burst where the plant produces reactive oxygen species at the site of the attempted invasion. ''U. maydis'' can respond to the oxidative burst with an oxidative stress response, regulated by the gene ''YAP1''. The response protects ''U. maydis'' from the host defense, and is necessary for the pathogen's virulence.<ref name=Molina2007/> Furthermore, ''U. maydis'' has a well-established recombinational DNA repair system which acts during mitosis and meiosis.<ref name=Kojic2006/> The system may assist the pathogen in surviving DNA damage arising from the host plant's oxidative defensive response to infection.<ref name=Michod2008/>

''Cryptococcus neoformans'' is an encapsulated yeast that can live in both plants and animals. ''C.{{nbsp}}neoformans'' usually infects the lungs, where it is phagocytosed by alveolar macrophages.<ref name=Fan2005/> Some ''C.{{nbsp}}neoformans'' can survive inside macrophages, which appears to be the basis for latency, disseminated disease, and resistance to antifungal agents. One mechanism by which ''C.{{nbsp}}neoformans'' survives the hostile macrophage environment is by up-regulating the expression of genes involved in the oxidative stress response.<ref name=Fan2005/> Another mechanism involves meiosis. The majority of ''C.{{nbsp}}neoformans'' are mating "type a". Filaments of mating "type a" ordinarily have haploid nuclei, but they can become diploid (perhaps by endoduplication or by stimulated nuclear fusion) to form blastospores. The diploid nuclei of blastospores can undergo meiosis, including recombination, to form haploid basidiospores that can be dispersed.<ref name=Lin2005/> This process is referred to as monokaryotic fruiting. This process requires a gene called ''DMC1'', which is a conserved homologue of genes ''recA'' in bacteria and ''RAD51'' in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus, ''C.{{nbsp}}neoformans'' can undergo a meiosis, monokaryotic fruiting, that promotes recombinational repair in the oxidative, DNA damaging environment of the host macrophage, and the repair capability may contribute to its virulence.<ref name=Michod2008/><ref name=Lin2005/>

==Human use== {{See also|Human interactions with fungi}} [[File:S cerevisiae under DIC microscopy.jpg|thumb|upright=0.85|right|alt=Microscopic view of five spherical structures; one of the spheres is considerably smaller than the rest and attached to one of the larger spheres|''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. Methods have been developed for genetic engineering of fungi,<ref name=Finsham1989/> enabling metabolic engineering of fungal species. For example, genetic modification of yeast species<ref name="Baghban et al. 2019"/>—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.<ref name=Huang2008/> Fungi-based industries are sometimes considered to be a major part of a growing bioeconomy, with applications under research and development including use for textiles, meat substitution and general fungal biotechnology.<ref>{{cite journal |last1=Meyer |first1=Vera |last2=Basenko |first2=Evelina Y. |last3=Benz |first3=J. Philipp |last4=Braus |first4=Gerhard H. |last5=Caddick |first5=Mark X. |last6=Csukai |first6=Michael |last7=de Vries |first7=Ronald P. |last8=Endy |first8=Drew |last9=Frisvad |first9=Jens C. |last10=Gunde-Cimerman |first10=Nina |last11=Haarmann |first11=Thomas |last12=Hadar |first12=Yitzhak |last13=Hansen |first13=Kim |last14=Johnson |first14=Robert I. |last15=Keller |first15=Nancy P. |last16=Kraševec |first16=Nada |last17=Mortensen |first17=Uffe H. |last18=Perez |first18=Rolando |last19=Ram |first19=Arthur F. J. |last20=Record |first20=Eric |last21=Ross |first21=Phil |last22=Shapaval |first22=Volha |last23=Steiniger |first23=Charlotte |last24=van den Brink |first24=Hans |last25=van Munster |first25=Jolanda |last26=Yarden |first26=Oded |last27=Wösten |first27=Han A. B. |title=Growing a circular economy with fungal biotechnology: a white paper |journal=Fungal Biology and Biotechnology |date=2 April 2020 |volume=7 |issue=1 |page=5 |doi=10.1186/s40694-020-00095-z |pmid=32280481 |pmc=7140391 |s2cid=215411291 |issn=2054-3085 |doi-access=free |title-link=doi}}</ref><ref>{{cite journal |last1=Jones |first1=Mitchell |last2=Gandia |first2=Antoni |last3=John |first3=Sabu |last4=Bismarck |first4=Alexander |title=Leather-like material biofabrication using fungi |journal=Nature Sustainability |date=January 2021 |volume=4 |issue=1 |pages=9–16 |doi=10.1038/s41893-020-00606-1 |s2cid=221522085 |language=en |issn=2398-9629}}</ref><ref>{{cite web |title=Plant-based meat substitutes - products with future potential {{!}} Bioökonomie.de |url=https://biooekonomie.de/en/topics/in-depth-reports/plant-based-meat-substitutes-products-future-potential |website=biooekonomie.de |access-date=25 May 2022 |language=en |archive-date=10 December 2023 |archive-url=https://web.archive.org/web/20231210014627/https://biooekonomie.de/en/topics/in-depth-reports/plant-based-meat-substitutes-products-future-potential |url-status=live }}</ref><ref>{{cite web |last1=Berlin |first1=Kustrim CerimiKustrim Cerimi studied biotechnology at the Technical University in |last2=biotechnology |first2=is currently doing his PhD He is interested in the broad field of fungal |last3=Artists |first3=Has Collaborated in Various Interdisciplinary Projects with |last4=Artists |first4=Hybrid |title=Mushroom meat substitutes: A brief patent overview |url=https://blogs.biomedcentral.com/on-biology/2022/01/28/mushroom-meat-substitutes-a-brief-patent-overview/ |website=On Biology |access-date=25 May 2022 |date=28 January 2022 |archive-date=29 November 2023 |archive-url=https://web.archive.org/web/20231129012028/https://blogs.biomedcentral.com/on-biology/2022/01/28/mushroom-meat-substitutes-a-brief-patent-overview/ |url-status=live }}</ref><ref>{{cite journal |last1=Lange |first1=Lene |title=The importance of fungi and mycology for addressing major global challenges* |journal=IMA Fungus |date=December 2014 |volume=5 |issue=2 |pages=463–471 |doi=10.5598/imafungus.2014.05.02.10 |pmid=25734035 |pmc=4329327 |issn=2210-6340}}</ref>

===Therapeutic uses=== [[File:Penicillium rubens (type specimen).png|thumb|The mold ''Penicillium rubens'' was the source of penicillin G.<ref name="pmid32973216">{{cite journal |vauthors=Pathak A, Nowell RW, Wilson CG, Ryan MJ, Barraclough TG |title=Comparative genomics of Alexander Fleming's original ''Penicillium'' isolate (IMI 15378) reveals sequence divergence of penicillin synthesis genes |date=September 2020 |journal=Scientific Reports |volume=10 |issue=1 |article-number=15705 |doi=10.1038/s41598-020-72584-5 |pmid=32973216 |pmc=7515868 |bibcode=2020NatSR..1015705P}}</ref>]]

====Modern chemotherapeutics==== {{See also|Medicinal fungi}} Many species produce metabolites that are major sources of pharmacologically active drugs.

=====Antibiotics===== Particularly important are the antibiotics, including the penicillins, a structurally related group of β-lactam antibiotics that are synthesized from small peptides.<ref>{{cite journal |last1=Bills |first1=Gerald F. |last2=Gloer |first2=James B. |title=Biologically Active Secondary Metabolites from the Fungi |journal=Microbiology Spectrum |date=2016 |volume=4 |issue=6 |article-number=4.6.01 |doi=10.1128/microbiolspec.funk-0009-2016 |pmid=27809954 }}</ref> 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.<ref name=Brakhage2004/> 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.<ref name=Pan2008/> Widespread use of antibiotics for the treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and others began in the early 20th century and continues to date. In nature, antibiotics of fungal or bacterial origin appear to play a dual role: at high concentrations they act as chemical defense against competition with other microorganisms in species-rich environments, such as the rhizosphere, and at low concentrations as quorum-sensing molecules for intra- or interspecies signaling.<ref name=Fajardo2008/>

=====Other===== Other drugs produced by fungi include griseofulvin isolated from ''Penicillium griseofulvum'', used to treat fungal infections,<ref name=Loo2006/> 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.<ref name=Manzoni2002/> Psilocybin from fungi is investigated for therapeutic use and appears to cause global increases in brain network integration.<ref>{{cite journal |last1=Daws |first1=Richard E. |last2=Timmermann |first2=Christopher |last3=Giribaldi |first3=Bruna |last4=Sexton |first4=James D. |last5=Wall |first5=Matthew B. |last6=Erritzoe |first6=David |last7=Roseman |first7=Leor |last8=Nutt |first8=David |last9=Carhart-Harris |first9=Robin |author9-link=Robin Carhart-Harris |title=Increased global integration in the brain after psilocybin therapy for depression |journal=Nature Medicine |date=April 2022 |volume=28 |issue=4 |pages=844–851 |doi=10.1038/s41591-022-01744-z |pmid=35411074 |s2cid=248099554 |language=en |issn=1546-170X |doi-access=free |title-link=doi |hdl=10044/1/95521 |hdl-access=free}}</ref> Fungi produce compounds that inhibit viruses<ref name=elMekkawy1998/><ref name=ElDine2008/> and cancer cells.<ref name=Hetland2008/> 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.<ref name=Sullivan2006/><ref name=Halpern2002/> In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from ''Trametes versicolor'', is an approved adjuvant for cancer therapy.<ref name="Fritz et al. 2015"/>

===Traditional medicine=== {{multiple image |align=right |image1=Ganoderma lucidum 01.jpg |width1=140 |alt1=Upper surface view of a kidney-shaped fungus, brownish-red with a lighter yellow-brown margin, and a somewhat varnished or shiny appearance |caption1= |image2=CordycepsSinensis.jpg |width2=180 |alt2=Two dried yellow-orange caterpillars, one with a curly grayish fungus growing out of one of its ends. The grayish fungus is roughly equal to or slightly greater in length than the caterpillar, and tapers in thickness to a narrow end. |caption2= |footer=The fungi ''Ganoderma lucidum'' (left) and ''Ophiocordyceps sinensis'' (right) are used in traditional medicine practices }}

Certain mushrooms are used as supposed therapeutics in folk medicine practices, such as traditional Chinese medicine. Mushrooms with a history of such use include ''Agaricus subrufescens'',<ref name=Hetland2008/><ref name=Firenzuoli2008/> ''Ganoderma lucidum'',<ref name="Lu et al. 2020"/> and ''Ophiocordyceps sinensis''.<ref name="Olatunji et al. 2018"/>

===Cultured foods=== Baker's yeast or ''Saccharomyces cerevisiae'', a unicellular fungus, is used to make bread and other wheat-based products, such as pizza dough and dumplings.<ref name=Kulp2000/> Yeast species of the genus ''Saccharomyces'' are also used to produce alcoholic beverages through fermentation.<ref name=Piskur2006/> Shoyu koji mold (''Aspergillus oryzae'') is an essential ingredient in brewing shoyu (soy sauce) and sake, and the preparation of miso,<ref name=Abe2006/> while ''Rhizopus'' species are used for making tempeh.<ref name=Hachmeister1993/> 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''.<ref name=Jorgensen2007/> Quorn, a meat alternative, is made from ''Fusarium venenatum''.<ref name=ODonnell1998/>

[[File:Asian mushrooms.jpg|thumb|upright=1.2|A selection of edible Asian fungi]] ===In food===

Edible mushrooms include commercially raised and wild-harvested fungi. ''Agaricus bisporus'', sold as button mushrooms when small or Portobello mushrooms when larger, is the most widely cultivated species in the West, used in salads, soups, and many other dishes. Many Asian fungi are commercially grown and have increased in popularity in the West. They are often available fresh in grocery stores and markets, including straw mushrooms (''Volvariella volvacea''), oyster mushrooms (''Pleurotus spp.''), shiitakes (''Lentinula edodes''), and enokitake (''Flammulina'' spp.).<ref name=Stamets2000/>

[[File:Blue Stilton Quarter Front.jpg|thumb|alt=A corner of cheese with greenish streaks through it|Stilton cheese veined with ''Penicillium roqueforti'']]

Many other mushroom species are harvested from the wild for personal consumption or commercial sale. Milkcap 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.{{sfn|Hall|2003|pp=13–26}}

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''.<ref name=Kinsella1976/> 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.<ref name=Erdogan2004/>

===Poisonous fungi=== [[File:Amanita phalloides 1.JPG|upright=0.75|thumb|alt=Two light yellow-green mushrooms with stems and caps, one smaller and still in the ground, the larger one pulled out and laid beside the other to show its bulbous stem with a ring|''Amanita phalloides'' accounts for the majority of fatal mushroom poisonings worldwide. It sometimes lacks the greenish color seen here.]]

Many mushroom species are poisonous to humans and cause a range of reactions including slight digestive problems, allergic reactions, hallucinations, severe organ failure, and death. Genera with mushrooms containing deadly toxins include, not are not limited to ''Conocybe'', ''Galerina'', ''Lepiota'' and infamously, ''Amanita''.<ref name=Orr1979/> The latter genus the death cap ''(A.{{nbsp}}phalloides)'', the most common cause of deadly mushroom poisoning. In particular, ''Amanita'' sect. ''Phalloideae'' contains dozens of amatoxin-containing species, including ''A. phalloides'' as well as the destroying angels.<ref name=Vetter1998/> The false morel (''Gyromitra esculenta'') is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.<ref name=Leathem2007/> ''Tricholoma equestre'' was considered edible until it was implicated in serious poisonings causing rhabdomyolysis.<ref name=KarlsonStiber2003/> Fly agaric mushrooms (''Amanita muscaria'') also cause occasional non-fatal poisonings, mostly as a result of ingestion 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 northeastern Siberia.<ref name=Michelot2003/>

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.{{sfn|Hall|2003|p=7}}<ref name=Ammirati1987/>

===Pest control=== {{Main|Biological pest control#Fungi}}

[[File:Beauveria.jpg|thumb|left|alt=Two dead grasshoppers with a whitish fuzz growing on them|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,<ref name=LopezGomez2006/> or if they are parasites of these pathogens. For example, certain species 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.<ref name="urlUSDA Biocontrol"/> 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.<ref name="Chandler 2017"/> Examples that have been used as biological insecticides are ''Beauveria bassiana'', ''Metarhizium'' spp., ''Hirsutella'' spp., ''Paecilomyces'' (''Isaria'') spp., and ''Lecanicillium lecanii''.<ref name=Deshpande1999/><ref name=Thomas2007/> Endophytic fungi of grasses of the genus ''Epichloë'', such as ''E.&nbsp;coenophiala'', 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.<ref name="Guerre 2015"/> Infecting cultivars of pasture or forage grasses with ''Epichloë'' 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.<ref name=Bouton2002/><ref name=Parish2003/>

===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.<ref name="Zhuo & Fan 2021"/> Fungi have been shown to biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.<ref name=BBC2008/><ref name=Fomina2007/><ref name=Fomina2008/>

===Model organisms=== Several pivotal discoveries in biology were made by researchers using fungi as model organisms, that is, fungi that grow and sexually reproduce rapidly in the laboratory. For example, the one gene-one enzyme hypothesis was formulated by scientists using the bread mold ''Neurospora crassa'' to test their biochemical theories.<ref name=Beadle1941/> Other important model fungi are ''Aspergillus nidulans'' and the yeasts ''Saccharomyces cerevisiae'' and ''Schizosaccharomyces pombe'', each of which with a long history of use to investigate issues in eukaryotic cell biology and genetics, such as cell cycle regulation, chromatin structure, and gene regulation. Other fungal models have emerged that address specific biological questions relevant to medicine, plant pathology, and industrial uses; examples include ''Candida albicans'', a dimorphic, opportunistic human pathogen,<ref name=Datta1989/> ''Magnaporthe grisea'', a plant pathogen,<ref name=Dean2005/> and ''Pichia pastoris'', a yeast widely used for eukaryotic protein production.<ref name="Karbalaei et al. 2020"/>

===Others=== Fungi are used extensively to produce industrial chemicals like citric, gluconic, lactic, and malic acids,<ref name=Schlegel1993/> and industrial enzymes, such as lipases used in biological detergents,<ref name=Joseph2008/> cellulases used in making cellulosic ethanol<ref name=Kumar2008/> and stonewashed jeans,<ref name=nysaes/> and amylases,<ref name=OlempskaBeer2006/> invertases, proteases, and xylanases.<ref name=Polizeli2005/>

==See also== {{Portal|Fungi}} {{div col}} * Balanophoraceae * ''Balanophora fungosa'' * Conservation of fungi * Fantastic Fungi * Glossary of mycology * Marine fungi * Fungal infection * Outline of fungi ** Outline of lichens * Fungi in art {{div col end}} {{clear}}

==References== ===Footnotes=== {{notelist}}

===Citations=== {{Reflist|refs=

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<ref name="Redhead & Norvell 2013">{{cite journal |last1=Redhead |first1=Scott |last2=Norvell |first2=Lorelei |year=2013 |title=MycoBank, Index Fungorum, and Fungal Names recommended as official nomenclatural repositories for 2013 |journal=IMA Fungus |volume=3 |issue=2 |pages=44–45 |url=https://www.researchgate.net/publication/255719633}}</ref>

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<ref name="Rhimi et al. 2020">{{cite journal |last1=Rhimi |first1=Wafa |last2=Theelen |first2=Bart |last3=Boekhout |first3=Teun |last4=Otranto |first4=Domenico |last5=Cafarchia |first5=Claudia |title=''Malassezia'' spp. yeasts of emerging concern in fungemia |journal=Frontiers in Cellular and Infection Microbiology |volume=10 |year=2020 |article-number=370 |doi=10.3389/fcimb.2020.00370 |pmid=32850475 |pmc=7399178 |doi-access=free |title-link=doi}}</ref>

<ref name="Rigling & Prospero 2018">{{cite journal |last1=Rigling |first1=Daniel |last2=Prospero |first2=Simone |title=''Cryphonectria parasitica'', the causal agent of chestnut blight: invasion history, population biology and disease control |journal=Molecular Plant Pathology |volume=19 |issue=1 |year=2018 |pages=7–20 |doi=10.1111/mpp.12542 |pmid=28142223 |pmc=6638123|bibcode=2018MolPP..19....7R }}</ref>

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<ref name="Rossman 2014">{{cite journal |last1=Rossman |first1=Amy Y. |title=Lessons learned from moving to one scientific name for fungi |journal=IMA Fungus |volume=5 |issue=1 |year=2014 |pages=81–89 |pmc=4107901 |pmid=25083410 |doi=10.5598/imafungus.2014.05.01.10}}</ref>

<ref name=Samuels2006>For an example, see {{cite journal |vauthors=Samuels GJ |title=''Trichoderma'': systematics, the sexual state, and ecology |journal=Phytopathology |volume=96 |issue=2 |pages=195–206 |date=February 2006 |pmid=18943925 |doi=10.1094/PHYTO-96-0195 |url=https://zenodo.org/record/1235933 |doi-access=free |title-link=doi|bibcode=2006PhPat..96..195S }}</ref>

<ref name=Sancho2007>{{cite journal |vauthors=Sancho LG, de la Torre R, Horneck G, Ascaso C, de Los Rios A, Pintado A, Wierzchos J, Schuster M |s2cid=4121180 |title=Lichens survive in space: results from the 2005 LICHENS experiment |journal=Astrobiology |volume=7 |issue=3 |pages=443–54 |date=June 2007 |pmid=17630840 |doi=10.1089/ast.2006.0046 |bibcode=2007AsBio...7..443S|hdl=10261/20262 |hdl-access=free }}</ref>

<ref name="Santini & Battisti 2019">{{cite journal |last1=Santini |first1=Alberto |last2=Battisti |first2=Andrea |title=Complex insect–pathogen interactions in tree pandemics |journal=Frontiers in Physiology |volume=10 |year=2019 |article-number=550 |doi=10.3389/fphys.2019.00550 |pmc=6517489 |pmid=31133880 |doi-access=free |title-link=doi}}</ref>

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===Cited literature=== {{refbegin}} * {{cite book |vauthors=Ainsworth GC |title=Introduction to the History of Mycology |publisher=Cambridge University Press |location=Cambridge, UK |year=1976 |isbn=978-0-521-11295-6}} * {{cite book |vauthors=Alexopoulos CJ, Mims CW, Blackwell M |title=Introductory Mycology |year=1996 |publisher=John Wiley & Sons |isbn=978-0-471-52229-4}} * {{cite book |vauthors=Deacon J |title=Fungal Biology |publisher=Blackwell Publishers |location=Cambridge, Massachusetts |year=2005 |isbn=978-1-4051-3066-0}} * {{cite book |vauthors=Hall IR |title=Edible and Poisonous Mushrooms of the World |publisher=Timber Press |location=Portland, Oregon |year=2003 |isbn=978-0-88192-586-9}} * {{cite book |vauthors=Hanson JR |title=The Chemistry of Fungi |year=2008 |publisher=Royal Society of Chemistry |isbn=978-0-85404-136-7}} * {{cite book |vauthors=Jennings DH, Lysek G |title=Fungal Biology: Understanding the Fungal Lifestyle |year=1996 |publisher=Bios Scientific Publishers Ltd |location=Guildford, UK |isbn=978-1-85996-150-6}} * {{cite book |vauthors=Kirk PM, Cannon PF, Minter DW, Stalpers JA |title=Dictionary of the Fungi |edition=10th |publisher=CAB International |location=Wallingford, UK |year=2008 |isbn=978-0-85199-826-8}} * {{cite book |vauthors=Taylor EL, Taylor TN |title=The Biology and Evolution of Fossil Plants |publisher=Prentice Hall |location=Englewood Cliffs, New Jersey |year=1993 |isbn=978-0-13-651589-0}} {{refend}}

==Further reading== * Kolbert, Elizabeth, "Spored to Death" (review of Emily Monosson, ''Blight: Fungi and the Coming Pandemic'', Norton, 253 pp.; and Alison Pouliot, ''Meetings with Remarkable Mushrooms: Forays with Fungi Across Hemispheres'', University of Chicago Press, 278 pp.), ''The New York Review of Books'', vol. LXX, no.14 (21 September 2023), pp.&nbsp;41–42. "Fungi sicken us and fungi sustain us. In either case, we ignore them at our peril." (p.&nbsp;42.) * Seifert, Keith. ''The Hidden Kingdom of Fungi''. Greystone Books, 2022. {{ISBN|978-1771646628}}.<ref>{{cite magazine |last=Wilkinson |first=Allie |title=Meet the fungal friends and foes that surround us |date=September 6, 2022 |magazine=Science News |url= https://www.sciencenews.org/article/fungi-hidden-kingdom-book-microfungi }}</ref>

==External links== {{Sister project links|c=Fungi |commonscat=Fungi |wikt=fungus |1=|author=|auto=|b=no |collapsible=|cookbook=|d=|display=|iw=|m=|mw=|n=no |position=|q=no |qid=|s=no |species=Fungi |species_author=|style=|v=no |voy=no}} * M. C. Cooke (1875), [https://www.gutenberg.org/ebooks/30181 Fungi: Their Nature and Uses], (2009) * ---- (1872), [https://www.gutenberg.org/ebooks/63416 Rust, Smut, Mildew, & Mould]: An Introduction to the Study of Microscopic Fungi, (2020)

{{Library resources box |onlinebooks=yes |by=no |lcheading=Fungi |label=Fungus }} * [http://tolweb.org/fungi Tree of Life web project: Fungi] {{Webarchive|url=https://web.archive.org/web/20210125081408/http://tolweb.org/fungi |date=25 January 2021}} * [https://www.eol.org/pages/5559 Encyclopedia of Life: Fungus] * [https://www.botanical-dermatology-database.info/BotDermFolder/FUNGI.html FUNGI] in [https://www.botanical-dermatology-database.info/index.html BoDD – Botanical Dermatology Database]

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