A characteristic that places fungi in a different kingdom fromplants,bacteria, and someprotists ischitin in theircell walls. Fungi, like animals, areheterotrophs; they acquire their food by absorbing dissolved molecules, typically by secretingdigestive enzymes into their environment. Fungi do notphotosynthesize. Growth is their means ofmobility, except forspores (a few of which areflagellated), which may travel through the air or water. Fungi are the principaldecomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named theEumycota (true fungi orEumycetes), that share acommon ancestor (i.e. they form amonophyletic group), an interpretation that is also strongly supported bymolecular phylogenetics. This fungal group is distinct from the structurally similarmyxomycetes (slime molds) andoomycetes (water molds). The discipline ofbiology devoted to the study of fungi is known asmycology (from theGreekμύκηςmykes, mushroom). In the past, mycology was regarded as a branch ofbotany, 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 theircryptic lifestyles in soil or on dead matter. Fungi includesymbionts of plants, animals, or other fungi and alsoparasites. They may become noticeable whenfruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrientcycling and exchange in the environment. They have long been used as a directsource of human food, in the form of mushrooms andtruffles; as aleavening agent for bread; and in thefermentation of various food products, such aswine,beer, andsoy sauce. Since the 1940s, fungi have been used for the production ofantibiotics, and, more recently, variousenzymes produced by fungi are usedindustrially and indetergents. Fungi are also used asbiological pesticides to control weeds, plant diseases, and insect pests. Many species producebioactive compounds calledmycotoxins, such asalkaloids andpolyketides, that are toxic to animals, including humans. The fruiting structures ofa few species containpsychotropic compounds and are consumedrecreationally or in traditionalspiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significantpathogens of humans and other animals. Losses of crops due to fungal diseases (e.g.,rice blast disease) orfood spoilage can have a large impact on humanfood supplies and local economies.
The fungus kingdom encompasses an enormous diversity oftaxa with varied ecologies,life cycle strategies, andmorphologies ranging from unicellular aquaticchytrids to large mushrooms. However, little is known of the truebiodiversity of the fungus kingdom, which has been estimated at 2.2 million to 3.8 million species.[7] Of these, only about 148,000 have been described,[8] with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans.[9] Ever since the pioneering 18th and 19th centurytaxonomical works ofCarl Linnaeus,Christiaan Hendrik Persoon, andElias Magnus Fries, fungi have been classified according to their morphology (e.g., characteristics such as spore color or microscopic features) orphysiology. Advances inmolecular genetics have opened the way forDNA 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 onesubkingdom, sevenphyla, and tensubphyla.
Etymology
The English wordfungus is directly adopted from theLatinfungus (mushroom), used in the writings ofHorace andPliny.[10] This in turn is derived from theGreek wordsphongos (σφόγγος 'sponge'), which refers to themacroscopic structures and morphology of mushrooms and molds;[11] theroot is also used in other languages, such as the GermanSchwamm ('sponge') andSchimmel ('mold').[12]
The wordmycology is derived from the Greekmykes (μύκης 'mushroom') andlogos (λόγος 'discourse').[13] It denotes the scientific study of fungi. The Latin adjectival form of "mycology" (mycologicæ) appeared as early as 1796 in a book on the subject byChristiaan Hendrik Persoon.[14] The word appeared in English as early as 1824 in a book byRobert Kaye Greville.[15] In 1836 the English naturalistMiles Joseph Berkeley's publicationThe English Flora of Sir James Edward Smith, Vol. 5. also refers to mycology as the study of fungi.[11][16]
A group of all the fungi present in a particular region is known asmycobiota (plural noun, no singular).[17] The termmycota is often used for this purpose, but many authors use it as a synonym of Fungi. The wordfunga has been proposed as a less ambiguous term morphologically similar tofauna andflora.[18] TheSpecies Survival Commission (SSC) of theInternational Union for Conservation of Nature (IUCN) in August 2021 asked that the phrasefauna and flora be replaced byfauna, flora, and funga.[19]
Before the introduction ofmolecular methods for phylogenetic analysis,taxonomists considered fungi to be members of theplant kingdom because of similarities in lifestyle: both fungi and plants are mainlyimmobile, and have similarities in general morphology and growth habitat. Although inaccurate, the common misconception that fungi are plants persists among the general public due to their historical classification, as well as several similarities.[20][21] Like plants, fungi often grow in soil and, in the case ofmushrooms, form conspicuousfruit bodies, which sometimes resemble plants such asmosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to havediverged around one billion years ago (around the start of theNeoproterozoic Era).[22][23] 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:
With plants: Fungi have a cell wall[27] andvacuoles.[28] They reproduce by both sexual and asexual means, and likebasal plant groups (such asferns andmosses) producespores. Similar to mosses and algae, fungi typically havehaploid nuclei.[29]
The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures calledhyphae, which may contain multiple nuclei and extend by growing at their tips. Each tip contains a set of aggregatedvesicles—cellular structures consisting ofproteins,lipids, and other organic molecules—called theSpitzenkörper.[32] Both fungi andoomycetes grow as filamentous hyphal cells.[33] In contrast, similar-looking organisms, such as filamentousgreen algae, grow by repeated cell division within a chain of cells.[25] There are also single-celled fungi (yeasts) that do not form hyphae, and some fungi have both hyphal and yeast forms.[34]
Some species grow as unicellular yeasts that reproduce bybudding orfission.Dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions.[34]
The fungal cell wall is made of achitin-glucan complex; whileglucans are also found in plants andchitin in theexoskeleton ofarthropods,[36] 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.[37][38]
Most fungi lack an efficient system for the long-distance transport of water and nutrients, such as thexylem andphloem in many plants. To overcome this limitation, some fungi, such asArmillaria, formrhizomorphs,[39] which resemble and perform functions similar to theroots of plants. As eukaryotes, fungi possess abiosynthetic pathway for producingterpenes that usesmevalonic acid andpyrophosphate aschemical building blocks.[40] Plants and some other organisms have an additional terpene biosynthesis pathway in their chloroplasts, a structure that fungi and animals do not have.[41] Fungi produce severalsecondary metabolites that are similar or identical in structure to those made by plants.[40] Many of the plant and fungal enzymes that make these compounds differ from each other insequence and other characteristics, which indicates separate origins andconvergent evolution of these enzymes in the fungi and plants.[40][42]
Fungi have a worldwide distribution, and grow in a wide range of habitats, including extreme environments such asdeserts or areas with high salt concentrations[43] orionizing radiation,[44] as well as indeep sea sediments.[45] Some can survive the intenseUV andcosmic radiation encountered during space travel.[46] Most grow in terrestrial environments, though several species live partly or solely in aquatic habitats, such as thechytrid fungiBatrachochytrium dendrobatidis andB. salamandrivorans,parasites that have been responsible for a worldwide decline inamphibian populations. These organisms spend part of their life cycle as a motilezoospore, enabling them to propel themselves through water and enter their amphibian host.[47] Other examples of aquatic fungi include those living inhydrothermal areas of the ocean.[48]
Widespread white fungus in wood chip mulch in anOklahoma garden[49]
As of 2020,[update] around 148,000 species of fungi have beendescribed bytaxonomists,[8] but the global biodiversity of the fungus kingdom is not fully understood.[50] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[7] 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.[8] The following year, 2,905 new species were described—the highest annual record of new fungus names.[51] In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based onmorphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.[52] Species may also be distinguished by theirbiochemical andphysiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction tochemical tests. Thebiological species concept discriminates species based on their ability tomate. The application ofmolecular tools, such asDNA sequencing and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates ofgenetic diversity within various taxonomic groups.[53]
Mycology is the branch ofbiology 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, andpsychotropic substances consumed for religious purposes, as well as their dangers, such as poisoning or infection. The field ofphytopathology, the study of plant diseases, is closely related because many plant pathogens are fungi.[54]
The use of fungi by humans dates back to prehistory;Ötzi the Iceman, a well-preserved mummy of a 5,300-year-oldNeolithic man found frozen in the Austrian Alps, carried two species ofpolypore mushrooms that may have been used astinder (Fomes fomentarius), or for medicinal purposes (Piptoporus betulinus).[55] Ancient peoples have used fungi as food sources—often unknowingly—for millennia, in the preparation of leavened bread and fermented juices. Some of the oldest written records contain references to the destruction of crops that were probably caused by pathogenic fungi.[56]
Most fungi grow ashyphae, which are cylindrical, thread-like structures 2–10μm 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 calledbranching, or occasionally growing hyphal tips fork, giving rise to two parallel-growing hyphae.[60] Hyphae also sometimes fuse when they come into contact, a process called hyphal fusion (oranastomosis). These growth processes lead to the development of amycelium, an interconnected network of hyphae.[34] Hyphae can be eitherseptate orcoenocytic. Septate hyphae are divided into compartments separated by cross walls (internal cell walls, called septa, that are formed atright angles to the cell wall giving the hypha its shape), with each compartment containing one or more nuclei; coenocytic hyphae are not compartmentalized.[61] Septa havepores that allowcytoplasm,organelles, and sometimes nuclei to pass through; an example is thedolipore septum in fungi of the phylum Basidiomycota.[62] Coenocytic hyphae are in essencemultinucleate supercells.[63]
Many species have developed specialized hyphal structures for nutrient uptake from living hosts; examples includehaustoria in plant-parasitic species of most fungal phyla,[64] andarbuscules of severalmycorrhizal fungi, which penetrate into the host cells to consume nutrients.[65]
Although fungi areopisthokonts—a grouping of evolutionarily related organisms broadly characterized by a single posteriorflagellum—all phyla except for thechytrids have lost their posterior flagella.[66] Fungi are unusual among the eukaryotes in having a cell wall that, in addition toglucans (e.g.,β-1,3-glucan) and other typical components, also contains thebiopolymer chitin.[38]
Fungal mycelia can become visible to the naked eye, for example, on various surfaces andsubstrates, such as damp walls and spoiled food, where they are commonly calledmolds. Mycelia grown on solidagar media in laboratorypetri dishes are usually referred to ascolonies. These colonies can exhibit growth shapes and colors (due to spores orpigmentation) that can be used as diagnostic features in the identification of species or groups.[67] Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of aclonal colony ofArmillaria solidipes, which extends over an area of more than 900ha (3.5 square miles), with an estimated age of nearly 9,000years.[68]
Theapothecium—a specialized structure important insexual reproduction in the ascomycetes—is a cup-shaped fruit body that is often macroscopic and holds thehymenium, a layer of tissue containing the spore-bearing cells.[69] The fruit bodies of the basidiomycetes (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well known asmushrooms.
Growth and physiology
Mold growth covering a decayingpeach. 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 highsurface area to volume ratios.[70] Hyphae are specifically adapted for growth on solid surfaces, and to invadesubstrates and tissues.[71] They can exert large penetrative mechanical forces; for example, manyplant pathogens, includingMagnaporthe grisea, form a structure called anappressorium that evolved to puncture plant tissues.[72] The pressure generated by the appressorium, directed against the plantepidermis, can exceed 8megapascals (1,200 psi).[72] The filamentous fungusPaecilomyces lilacinus uses a similar structure to penetrate the eggs ofnematodes.[73]
The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellularturgor by producingosmolytes such asglycerol.[74] Adaptations such as these are complemented byhydrolytic enzymes secreted into the environment to digest large organic molecules—such aspolysaccharides,proteins, andlipids—into smaller molecules that may then be absorbed as nutrients.[75][76][77] The vast majority of filamentous fungi grow in a polar fashion (extending in one direction) by elongation at the tip (apex) of the hypha.[78] Other forms of fungal growth include intercalary extension (longitudinal expansion of hyphal compartments that are below the apex) as in the case of someendophytic fungi,[79] or growth by volume expansion during the development of mushroomstipes and other large organs.[80] Growth of fungi asmulticellular structures consisting ofsomatic and reproductive cells—a feature independently evolved in animals and plants[81]—has several functions, including the development of fruit bodies for dissemination of sexual spores (see above) andbiofilms for substrate colonization andintercellular communication.[82]
Fungi are traditionally consideredheterotrophs, organisms that rely solely oncarbon fixed by other organisms formetabolism. Fungi haveevolved a high degree of metabolic versatility that allows them to use a diverse range of organic substrates for growth, including simple compounds such asnitrate,ammonia,acetate, orethanol.[83][84] In some species the pigmentmelanin may play a role in extracting energy fromionizing radiation, such asgamma radiation. This form of "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlyingbiophysical and biochemical processes are not well known.[44] This process might bear similarity to CO2 fixation viavisible light, but instead uses ionizing radiation as a source of energy.[85]
Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms.[86] 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 thelife cycle of a species, theteleomorph (sexual reproduction) and theanamorph (asexual reproduction).[87] 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-containingpropagules.
Asexual reproduction
Asexual reproduction occurs via vegetative spores (conidia) or throughmycelial fragmentation. Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each component grows into a separate mycelium. Mycelial fragmentation and vegetative spores maintainclonal populations adapted to a specificniche, and allow more rapid dispersal than sexual reproduction.[88] The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) orDeuteromycota comprise all the species that lack an observable sexual cycle.[89] 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.[90]
Sexual reproduction withmeiosis has been directly observed in all fungal phyla exceptGlomeromycota[91] (genetic analysis suggests meiosis in Glomeromycota as well). It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and can be used to discriminate species by morphological differences in sexual structures and reproductive strategies.[92][93] Mating experiments between fungal isolates may identify species on the basis of biological species concepts.[93] 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 andbasidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Fungi employ twomating systems:heterothallic species allow mating only between individuals of the oppositemating type, whereashomothallic species can mate, and sexually reproduce, with any other individual or itself.[94]
Most fungi have both ahaploid and adiploid 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 adikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells (seeheterokaryosis).[95]
In ascomycetes, dikaryotic hyphae of thehymenium (the spore-bearing tissue layer) form a characteristichook (crozier) at the hyphal septum. Duringcell division, the formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (pluralasci) is then formed, in whichkaryogamy (nuclear fusion) occurs. Asci are embedded in anascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production ofascospores. After dispersal, the ascospores may germinate and form a new haploid mycelium.[96]
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 aclamp 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.[97] Abasidiocarp is formed in which club-like structures known asbasidia generate haploidbasidiospores after karyogamy and meiosis.[98] The most commonly known basidiocarps are mushrooms, but they may also take other forms (seeMorphology section).
In fungi formerly classified asZygomycota, haploid hyphae of two individuals fuse, forming agametangium, a specialized cell structure that becomes a fertilegamete-producing cell. The gametangium develops into azygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoesmeiosis, generating new haploid hyphae, which may then form asexualsporangiospores. These sporangiospores allow the fungus to rapidly disperse and germinate into new genetically identical haploid fungal mycelia.[99]
Spore dispersal
The spores of most of the researched species of fungi are transported by wind.[100][101] Such species often produce dry orhydrophobic spores that do not absorb water and are readily scattered by raindrops, for example.[100][102][103] 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.
Specialized mechanical and physiological mechanisms, as well as spore surface structures (such ashydrophobins), enable efficient spore ejection.[104] For example, the structure of thespore-bearing cells in some ascomycete species is such that the buildup ofsubstances affecting cell volume and fluid balance enables the explosive discharge of spores into the air.[105] The forcible discharge of single spores termedballistospores involves formation of a small drop of water (Buller's drop), which upon contact with the spore leads to its projectile release with an initial acceleration of more than 10,000g;[106] the net result is that the spore is ejected 0.01–0.02cm, sufficient distance for it to fall through thegills orpores into the air below.[107] Other fungi, like thepuffballs, rely on alternative mechanisms for spore release, such as external mechanical forces. Thehydnoid fungi (tooth fungi) produce spores on pendant, tooth-like or spine-like projections.[108] Thebird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies.[109] Another strategy is seen in thestinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.[110]
Besides regular sexual reproduction with meiosis, certain fungi, such as those in the generaPenicillium andAspergillus, may exchange genetic material viaparasexual processes, initiated by anastomosis between hyphae andplasmogamy of fungal cells.[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[116] and is likely required for hybridization between species, which has been associated with major events in fungal evolution.[117]
In contrast toplants andanimals, 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 fungalfruiting 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 resembleextant fungi.[118] Often recovered from apermineralized plant or animal host, these samples are typically studied by making thin-section preparations that can be examined withlight microscopy ortransmission electron microscopy.[119] Researchers studycompression fossils by dissolving the surrounding matrix with acid and then using light orscanning electron microscopy to examine surface details.[120]
The earliest fossils possessing features typical of fungi date to thePaleoproterozoic era, some2,400 million years ago (Ma); these multicellularbenthic organisms had filamentous structures capable ofanastomosis.[121] Other studies (2009) estimate the arrival of fungal organisms at about 760–1060Ma on the basis of comparisons of the rate of evolution in closely related groups.[122] The oldest fossilizied mycelium to be identified from its molecular composition is between 715 and 810 million years old.[123] For much of thePaleozoic Era (542–251Ma), the fungi appear to have been aquatic and consisted of organisms similar to the extantchytrids in having flagellum-bearing spores.[124] The evolutionary adaptation from an aquatic to a terrestrial lifestyle necessitated a diversification of ecological strategies for obtaining nutrients, includingparasitism,saprobism, and the development ofmutualistic relationships such asmycorrhiza and lichenization.[125] Studies suggest that the ancestral ecological state of theAscomycota was saprobism, and that independentlichenization events have occurred multiple times.[126]
In May 2019, scientists reported the discovery of afossilized fungus, namedOurasphaira giraldae, in theCanadian Arctic, that may have grown on land a billion years ago, well beforeplants were living on land.[127][128][129]Pyritized fungus-likemicrofossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) have been reported in South China.[130] Earlier, it had been presumed that the fungi colonized the land during theCambrian (542–488.3Ma), also long before land plants.[131] Fossilized hyphae and spores recovered from theOrdovician of Wisconsin (460Ma) resemble modern-dayGlomerales, and existed at a time when the land flora likely consisted of only non-vascularbryophyte-like plants.[132]Prototaxites, which was probably a fungus or lichen, would have been the tallest organism of the lateSilurian and earlyDevonian. Fungal fossils do not become common and uncontroversial until the earlyDevonian (416–359.2Ma), when they occur abundantly in theRhynie chert, mostly asZygomycota andChytridiomycota.[131][133][134] At about this same time, approximately 400Ma, the Ascomycota and Basidiomycota diverged,[135] and all modernclasses of fungi were present by the LateCarboniferous (Pennsylvanian, 318.1–299Ma).[136]
Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 415Ma;[137] this date roughly corresponds to the age of the oldest knownsporocarp fossil, aPaleopyrenomycites species found in the Rhynie Chert.[138] The oldest fossil with microscopic features resembling modern-day basidiomycetes isPalaeoancistrus, found permineralized with afern from the Pennsylvanian.[139] Rare in the fossil record are the Homobasidiomycetes (ataxon roughly equivalent to the mushroom-producing species of theAgaricomycetes). Twoamber-preserved specimens provide evidence that the earliest known mushroom-forming fungi (the extinct speciesArchaeomarasmius leggetti) appeared during the lateCretaceous, 90Ma.[140][141]
Some time after thePermian–Triassic extinction event (251.4Ma), a fungal spike (originally thought to be an extraordinary abundance of fungal spores insediments) formed, suggesting that fungi were the dominant life form at this time, representing nearly 100% of the availablefossil record for this period.[142] However, the relative proportion of fungal spores relative to spores formed byalgal species is difficult to assess,[143] the spike did not appear worldwide,[144][145] and in many places it did not fall on the Permian–Triassic boundary.[146]
Sixty-five million years ago, immediately after theCretaceous–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".[147]
Taxonomy
Although commonly included in botany curricula and textbooks, fungi are more closely related toanimals than to plants and are placed with the animals in themonophyletic group ofopisthokonts.[148] Analyses usingmolecular phylogenetics support amonophyletic origin of fungi.[53][149] Thetaxonomy 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 experimentalmatings.[150]
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 consistentnomenclature.[53][151] Until relatively recent (2012) changes to theInternational 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.[152] Web sites such asIndex Fungorum andMycoBank are officially recognizednomenclatural repositories and list current names of fungal species (with cross-references to oldersynonyms).[153]
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.[53] It recognizes sevenphyla, two of which—the Ascomycota and the Basidiomycota—are contained within a branch representingsubkingdomDikarya, 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 accompanyingcladogram depicts the major fungaltaxa and their relationship to opisthokont and unikont organisms, based on the work of Philippe Silar,[154] "The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research"[155] and Tedersoo et al. 2018.[156] The lengths of the branches are not proportional toevolutionary distances.
Phylogenetic analysis has demonstrated that theMicrosporidia, unicellular parasites of animals and protists, are fairly recent and highly derivedendobiotic fungi (living within the tissue of another species).[124] Previously considered to be "primitive" protozoa, they are now thought to be either abasal branch of the Fungi, or asister group–each other's closest evolutionary relative.[158]
TheBlastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. Molecular data andultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basidiomycota). The blastocladiomycetes aresaprotrophs, feeding on decomposing organic matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids, most of which exhibitzygotic meiosis, the blastocladiomycetes undergosporic meiosis.[124]
TheNeocallimastigomycota were earlier placed in the phylum Chytridiomycota. Members of this small phylum areanaerobic 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).[160] They lackmitochondria but containhydrogenosomes of mitochondrial origin. As in the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.[53]
Arbuscular mycorrhiza seen under microscope.Flax root cortical cells containing paired arbuscules.Diagram of anapothecium (the typical cup-like reproductive structure of ascomycetes) showing sterile tissues as well as developing and mature asci
Members of theGlomeromycota formarbuscular mycorrhizae, a form of mutualistsymbiosis wherein fungal hyphae invade plant root cells and both species benefit from the resulting increased supply of nutrients. All known Glomeromycota species reproduce asexually.[91] The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago.[161] Formerly part of theZygomycota (commonly known as 'sugar' and 'pin' molds), the Glomeromycota were elevated to phylum status in 2001 and now replace the older phylum Zygomycota.[162] Fungi that were placed in the Zygomycota are now being reassigned to the Glomeromycota, or the subphylaincertae sedisMucoromycotina,Kickxellomycotina, theZoopagomycotina and theEntomophthoromycotina.[53] Some well-known examples of fungi formerly in the Zygomycota include black bread mold (Rhizopus stolonifer), andPilobolus species, capable of ejectingspores several meters through the air.[163] Medically relevant genera includeMucor,Rhizomucor, andRhizopus.[164]
TheAscomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota.[52] These fungi form meiotic spores calledascospores, which are enclosed in a special sac-like structure called anascus. This phylum includesmorels, a fewmushrooms andtruffles, unicellularyeasts (e.g., of the generaSaccharomyces,Kluyveromyces,Pichia, andCandida), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes includeAspergillus,Penicillium,Fusarium, andClaviceps. Many ascomycete species have only been observed undergoing asexual reproduction (calledanamorphic species), but analysis of molecular data has often been able to identify their closestteleomorphs in the Ascomycota.[165] 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).[166]
Unlike true fungi, thecell walls of oomycetes containcellulose and lackchitin. 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 inmycology textbooks and primary research literature.[171]
TheRozellida clade, including the "ex-chytrid"Rozella, is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi.[157] 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.[149]
Thenucleariids may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom.[148]ManyActinomycetales (Actinomycetota), a group with many filamentous bacteria, were also long believed to be fungi.[172][173]
Ecology
A pin mold decomposing a peach
Although often inconspicuous, fungi occur in every environment onEarth and play very important roles in mostecosystems. Along with bacteria, fungi are the majordecomposers in most terrestrial (and some aquatic) ecosystems, and therefore play a critical role inbiogeochemical cycles[174] and in manyfood webs. As decomposers, they play an essential role innutrient cycling, especially assaprotrophs andsymbionts, degradingorganic matter to inorganic molecules, which can then re-enter anabolic metabolic pathways in plants or other organisms.[175][176]
Symbiosis
Many fungi have importantsymbiotic relationships with organisms from most if not allkingdoms.[177][178][179] These interactions can bemutualistic or antagonistic in nature, or in the case ofcommensal fungi are of no apparent benefit or detriment to the host.[180][181][182]
With plants
Mycorrhizal symbiosis betweenplants 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.[183]
The mycorrhizal symbiosis is ancient, dating back to at least 400 million years.[161] It often increases the plant's uptake of inorganic compounds, such asnitrate andphosphate from soils having low concentrations of these key plant nutrients.[175][184] The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients.[185] Such mycorrhizal communities are called "commonmycorrhizal networks".[186][187] A special case of mycorrhiza ismyco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont.[188] Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.[189] 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.[190]
Lichens are a symbiotic relationship between fungi andphotosyntheticalgae orcyanobacteria. 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 ofascomycetes and a fewbasidiomycetes.[191] Lichens occur in every ecosystem on all continents, play a key role insoil formation and the initiation ofbiological succession,[192] and are prominent in some extreme environments, includingpolar,alpine, andsemiarid desert regions.[193] They are able to grow on inhospitable surfaces, including bare soil, rocks,tree bark, wood, shells, barnacles and leaves.[194] As inmycorrhizas, the photobiont provides sugars and other carbohydrates viaphotosynthesis 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.[195] Lichenization is a common mode of nutrition for fungi; around 27% of known fungi—more than 19,400 species—are lichenized.[196] Characteristics common to most lichens include obtainingorganic 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 ofdesiccation than most other photosynthetic organisms in the same habitat.[197]
With insects
Many insects also engage inmutualistic relationships with fungi. Several groups of ants cultivate fungi in the orderChaetothyriales for several purposes: as a food source, as a structural component of their nests, and as a part of an ant/plant symbiosis in thedomatia (tiny chambers in plants that house arthropods).[198]Ambrosia beetles cultivate various species of fungi in the bark of trees that they infest.[199] Likewise, females of severalwood wasp species (genusSirex) inject their eggs together with spores of the wood-rotting fungusAmylostereum areolatum into thesapwood ofpine trees; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae.[200] At least one species ofstingless bee has a relationship with a fungus in the genusMonascus, where the larvae consume and depend on fungus transferred from old to new nests.[201]Termites on the Africansavannah are also known to cultivate fungi,[177] and yeasts of the generaCandida andLachancea inhabit thegut of a wide range of insects, includingneuropterans,beetles, andcockroaches; it is not known whether these fungi benefit their hosts.[202] Fungi growing indead wood are essential forxylophagous insects (e.g.woodboring beetles).[203][204][205] They deliver nutrients needed byxylophages to nutritionally scarce dead wood.[206][204][205] Thanks to this nutritional enrichment the larvae of the woodboring insect is able to grow and develop to adulthood.[203] The larvae of many families offungicolous flies, particularly those within the superfamilySciaroidea such as theMycetophilidae and someKeroplatidae feed on fungal fruiting bodies and sterilemycorrhizae.[207]
The plant pathogenPuccinia magellanicum (calafate rust) causes the defect known aswitch's broom, seen here on abarberry shrub in Chile.Gram stain ofCandida albicans from a vaginal swab from a woman withcandidiasis, showing hyphae, and chlamydospores, which are 2–4μm in diameter
Organisms that parasitize fungi are known asmycoparasitic organisms. About 300 species of fungi and fungus-like organisms, belonging to 13 classes and 113 genera, are used asbiocontrol agents against plant fungal diseases.[220] Fungi can also act as mycoparasites or antagonists of other fungi, such asHypomyces chrysospermus, which grows onbolete mushrooms.Fungi can also become the target of infection bymycoviruses.[221][222]
Mycotoxins are secondary metabolites (ornatural products), and research has established the existence of biochemical pathways solely for the purpose of producing mycotoxins and other natural products in fungi.[40] Mycotoxins may providefitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory).[228][229] Many fungal secondary metabolites (or derivatives) are used medically, as described underHuman use below.
Pathogenic mechanisms
Ustilago maydis is a pathogenic plant fungus that causes smut disease in maize andteosinte. Plants have evolved efficient defense systems against pathogenic microbes such asU. maydis. A rapid defense reaction after pathogen attack is theoxidative burst where the plant producesreactive 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 geneYAP1. The response protectsU. maydis from the host defense, and is necessary for the pathogen's virulence.[230] Furthermore,U. maydis has a well-established recombinationalDNA repair system which acts during mitosis and meiosis.[231] The system may assist the pathogen in surviving DNA damage arising from the host plant's oxidative defensive response to infection.[232]
Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals.C.neoformans usually infects the lungs, where it is phagocytosed byalveolar macrophages.[233] SomeC.neoformans can surviveinside macrophages, which appears to be the basis forlatency, disseminated disease, and resistance to antifungal agents. One mechanism by whichC.neoformans survives the hostile macrophage environment is by up-regulating the expression of genes involved in the oxidative stress response.[233] Another mechanism involvesmeiosis. The majority ofC.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 formblastospores. The diploid nuclei of blastospores can undergo meiosis, including recombination, to form haploid basidiospores that can be dispersed.[234] This process is referred to as monokaryotic fruiting. This process requires a gene calledDMC1, which is a conserved homologue of genesrecA in bacteria andRAD51 in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus,C.neoformans can undergo a meiosis, monokaryotic fruiting, that promotes recombinational repair in the oxidative, DNA damaging environment of the host macrophage, and the repair capability may contribute to its virulence.[232][234]
The human use of fungi for food preparation or preservation and other purposes is extensive and has a long history.Mushroom farming andmushroom gathering are large industries in many countries. The study of the historical uses and sociological impact of fungi is known asethnomycology. Because of the capacity of this group to produce an enormous range ofnatural products withantimicrobial or other biological activities, many species have long been used or are being developed for industrialproduction of antibiotics, vitamins, andanti-cancer andcholesterol-lowering drugs. Methods have been developed forgenetic engineering of fungi,[235] enablingmetabolic engineering of fungal species. For example, genetic modification of yeast species[236]—which are easy to grow at fast rates in large fermentation vessels—has opened up ways ofpharmaceutical production that are potentially more efficient than production by the original source organisms.[237] Fungi-based industries are sometimes considered to be a major part of a growingbioeconomy, with applications underresearch and development including use for textiles,meat substitution and general fungal biotechnology.[238][239][240][241][242]
Many species produce metabolites that are major sources ofpharmacologically active drugs.
Antibiotics
Particularly important are the antibiotics, including thepenicillins, a structurally related group ofβ-lactam antibiotics that are synthesized from smallpeptides. Although naturally occurring penicillins such aspenicillin G (produced byPenicillium chrysogenum) have a relatively narrow spectrum of biological activity, a wide range of other penicillins can be produced bychemical modification of the natural penicillins. Modern penicillins aresemisynthetic compounds, obtained initially fromfermentation cultures, but then structurally altered for specific desirable properties.[244] Other antibiotics produced by fungi include:ciclosporin, commonly used as animmunosuppressant duringtransplant surgery; andfusidic acid, used to help control infection frommethicillin-resistantStaphylococcus aureus bacteria.[245] Widespread use of antibiotics for the treatment of bacterial diseases, such astuberculosis,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 therhizosphere, and at low concentrations asquorum-sensing molecules for intra- or interspecies signaling.[246]
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 ingrocery stores and markets, including straw mushrooms (Volvariella volvacea), oyster mushrooms (Pleurotus ostreatus), shiitakes (Lentinula edodes), andenokitake (Flammulina spp.).[265]
Certain types of cheeses require inoculation of milk curds with fungal species that impart a unique flavor and texture to the cheese. Examples include theblue color in cheeses such asStilton orRoquefort, which are made by inoculation withPenicillium roqueforti.[267] 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.[268]
Many mushroom species arepoisonous 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 includeConocybe,Galerina,Lepiota and the most infamous,Amanita.[269] The latter genus includes the destroying angel(A.virosa) and the death cap(A.phalloides), the most common cause of deadly mushroom poisoning.[270] The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.[271]Tricholoma equestre was considered edible until it was implicated in serious poisonings causingrhabdomyolysis.[272]Fly agaric mushrooms (Amanita muscaria) also cause occasional non-fatal poisonings, mostly as a result of ingestion for itshallucinogenic properties. Historically, fly agaric was used by different peoples in Europe and Asia and its present usage for religious orshamanic purposes is reported from some ethnic groups such as theKoryak people of northeasternSiberia.[273]
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.[274][275]
In agriculture, fungi may be useful if they actively compete for nutrients and space withpathogenic microorganisms such as bacteria or other fungi via thecompetitive exclusion principle,[276] or if they areparasites 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 importantcrop plants.[277] This has generated strong interest in practical applications that use these fungi in thebiological control of these agricultural pests.Entomopathogenic fungi can be used asbiopesticides, as they actively kill insects.[278] Examples that have been used asbiological insecticides areBeauveria bassiana,Metarhizium spp.,Hirsutella spp.,Paecilomyces (Isaria) spp., andLecanicillium lecanii.[279][280]Endophytic fungi of grasses of the genusEpichloë, such asE. coenophiala, produce alkaloids that are toxic to a range of invertebrate and vertebrateherbivores. These alkaloids protect grass plants fromherbivory, but several endophyte alkaloids can poison grazing animals, such as cattle and sheep.[281] Infecting cultivars ofpasture orforage grasses withEpichloë endophytes is one approach being used ingrass 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.[282][283]
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Further reading
Kolbert, Elizabeth, "Spored to Death" (review ofEmily Monosson,Blight: Fungi and the Coming Pandemic, Norton, 253 pp.; andAlison 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. 41–42. "Fungi sicken us and fungi sustain us. In either case, we ignore them at our peril." (p. 42.)
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