Fungus
| Fungi Fossil range: Early Devonian - Recent (but see text), | ||||||
|---|---|---|---|---|---|---|
 Clockwise from top left: Amanita muscaria, a basidiomycete; Sarcoscypha coccinea, an ascomycete; black bread mold, a zygomycete; a chytrid; a Aspergillus conidiophore. | ||||||
| Scientific classification | ||||||
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| Subkingdoms/Phyla | ||||||
| Dikarya (inc. Deuteromycota) |
A fungus (pronounced /ˈfʌŋɡəs/) is a eukaryotic organism that is a member of the kingdom Fungi (pronounced /ˈfʌndʒaɪ/ or /ˈfʌŋɡaɪ/).[2] The fungi are a monophyletic group, also called the Eumycota (true fungi or Eumycetes), that is phylogenetically distinct from the morphologically similar slime molds (myxomycetes) and water molds (oomycetes). The fungi are heterotrophic organisms possessing a chitinous cell wall, with most species growing as multicellular filaments called hyphae forming a mycelium; some species also grow as single cells. Sexual and asexual reproduction of the fungi is commonly via spores, often produced on specialized structures or in fruiting bodies. Some have lost the ability to form reproductive structures, and propagate solely by vegetative growth. Yeasts, molds, and mushrooms are examples of fungi. The discipline of biology devoted to the study of fungi is known as mycology, and is often regarded as a branch of botany, even though fungi are more closely related to animals than to plants.
Occurring worldwide, most fungi are largely invisible to the naked eye, living for the most part in soil, dead matter, and as symbionts of plants, animals, or other fungi. They perform an essential role in ecosystems in decomposing organic matter and are indispensable in nutrient cycling and exchange. Fungi may become noticeable when fruiting, either as mushrooms or molds. They have long been used as a direct source of food, such as mushrooms and truffles, and in fermentation of various food products, such as wine, beer, and soy sauce. More recently, fungi are being used as sources for antibiotics used in medicine and various enzymes, such as cellulases, pectinases, and proteases, important for industrial use or as active ingredients of detergents. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides that are toxic to animals including humans. Fruiting structures of a few species are used recreationally or in traditional ceremonies as a source of psychotropic compounds. Fungi are significant pathogens of humans and other animals, and losses due to diseases of crops (e.g., rice blast disease) or food spoilage can have a large impact on human food supply and local economies.
Etymology
The English word fungus is directly adopted from the Latin fungus, meaning "mushroom", used in Horace and Pliny.[3] This in turn is derived from the Greek word sphongos/σφογγος ("sponge"), referring to the macroscopic structures and morphology of mushrooms and molds, and this root is also used in other languages (e.g., the German Schwamm ("sponge"), Schimmel ("mold"), or Schwammerl for certain types of mushrooms).[4] The use of the word mycology (derived from the Greek mykes/μύκης meaning "mushroom" and logos/λόγος meaning "discourse")[5] to denote the scientific study of fungi is thought to have originated in 1836 with English naturalist Miles Joseph Berkeley in his publication The English Flora of Sir James Edward Smith, Vol. 5.[4]
Characteristics
The fungal kindom is defined by a number of features, some of which are shared with other organisms while others are unique to the fungi:
Shared features:
- With other eukaryotes: Fungi are eukaryotic, containing membrane-bound nuclei with chromosomes. Cells contain membrane-bound cytoplasmic organelles, DNA with noncoding regions called introns, sterol-containing membranes, and ribosomes of the 80S type.[6] Fungi have a characteristic range of soluble carbohydrates and storage compounds, including mannitol and other sugar alcohols, trehalose and glycogen the latter of which is also found in animals.[7]
- With animals: Fungi lack chloroplasts and are heterotrophic organisms, requiring preformed organic compounds as energy sources and also as carbon skeletons for organic synthesis.[8]
- With plants: Fungi possess a cell wall [9] and vacuoles. [10] 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.[11]
- With prokaryotes: As in some bacteria, biosynthesis of the amino acid L-lysine is via the α-aminoadipate pathway.[12]
Unique features:
- Fungi typically grow as hyphae, which extend at their tips.[13] This apical growth form is shared with the structurally similar oomycetes[14] and is in contrast with other filamentous organisms, like filamentous green algae, which grow by repeated cell divisions within a chain of cells (intercalary growth).[7]
- Some species grow as single-celled yeasts which reproduce by budding, and dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions.[15]
- The fungal cell wall contains glucans also found in plants, but also chitin not found in the Plant kingdom, but in the exoskeleton of arthropods.[16] In contrast to plants and the oomycetes, fungal cell walls do not contain cellulose.[17]
- Fungal hyphae may have multiple nuclei within each hyphal compartment,[11] and many budding yeasts are diploid.[18]
Diversity
Fungi have a worldwide distribution, and grow in a wide range of habitats, including deserts, hypersaline environments,[19] the deep sea,[20] on rocks,[21] and in extremely low and high temperatures. They are able to survive the intense UV and cosmic radiation encountered during space travel.[22] Most grow in terrestrial environments, but several species live partly or solely in aquatic habitats. For example, the chytrid fungus Batrachochytrium dendrobatidis—responsible for a worldwide decline in amphibian populations—spends part of its life cycle as motile zoospore, enabling it to propel itself through water and penetrate the skin of an amphibian host.[23]
Fungi, along with bacteria, are the primary decomposers of organic matter in most if not all terrestrial ecosystems worldwide. Based on observations of the ratio of the number of fungal species to the number of plant species in select environments, the fungal kingdom has been estimated to contain about 1.5 million species.[24] Around 70,000 species have been formally described by taxonomists, but the true dimension of fungal diversity is still unknown.[25] Until recently, fungal species were described based mainly on morphological characteristics, such as the size and shape of spores or fruiting structures, and biological species concepts. 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.[26]
Morphology
Microscopic structures
Although fungi are part of the opisthokont clade, all phyla except for the chytrids have lost their posterior flagella.[27] Fungi are unusual among the eukaryotes in having a cell wall that, besides glucans (e.g., β-1,3-glucan) and other typical components, contains the biopolymer chitin.[28]
Most fungi grow as thread-like filamentous microscopic structures called hyphae, and an assemblage of intertwined and interconnected hyphae is called a mycelium.[29] Hyphae can be septate, i.e., divided into compartments separated by a septum, each compartment containing one or more nuclei, or can be coenocytic, i.e., lacking hyphal compartmentalization.[30] However, septa have pores, such as the doliporus in the basidiomycetes that allow cytoplasm, organelles, and sometimes nuclei to pass through.[31] Coenocytic hyphae are essentially multinucleate supercells.[32] Several species have developed specialized structures for nutrient uptake from living hosts; examples include haustoria in plant parasites of most divisions, and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients.[33]
Macroscopic structures
Fungal mycelia can become visible macroscopically, for example, as concentric rings on various surfaces, such as damp walls, and on other substrates, such as spoilt food, and are commonly and generically called mould (American spelling, mold); mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies, exhibiting characteristic macroscopic growth shapes and colors, due to spores or pigmentation.[34]
Specialized structures important in sexual reproduction are the apothecia, perithecia, and cleistothecia in the ascomycetes,[35] and the fruiting bodies of the basidiomycetes and some ascomycetes. These reproductive structures can sometimes grow very large, and are well-known as mushrooms.
Growth and physiology
Growth as filamentous hyphae on or in solid substrates or single cells in aquatic environments is adapted to efficient extraction of nutrients from these environments, because these growth forms have high surface area to volume ratios. Hyphae are specifically adapted to growth on solid surfaces and within substrates, and can exert large penetrative mechanical forces. The plant pathogen, Magnaporthe grisea, forms a structure called an appressorium specifically designed for penetration of plant tissues. The pressure generated by the appressorium, which is directed against the plant epidermis, can exceed 8 MPa (80 bars).[36] A similar method is employed by the filamentous fungus Paecilomyces lilacinus to penetrate the eggs of plant-parasitic nematodes.[37] The generation of these mechanical pressures is the result of an interplay between physiological processes to increase intracellular turgor by production of osmolytes such as glycerol, and the morphology of the appressorium.[38] These adaptations in morphology are complemented by hydrolytic enzymes secreted into the environment for digestion of large organic molecules, such as polysaccharides, proteins, lipids, and other organic substrates into smaller molecules that may then be absorbed as nutrients.[39][40][41]
Traditionally, the fungi are considered heterotrophs, organisms that rely solely on carbon fixed by other organisms for metabolism. Fungi have evolved a remarkable metabolic versatility that allows them to use a diverse range of organic substrates for growth, including simple compounds as nitrate, ammonia, acetate, or ethanol.[42][43] Certain species seem to be able to utilize the pigment melanin to extract energy from ionizing radiation, such as gamma radiation, for "radiotrophic" growth.[44] This process might bear similarity to CO2 fixation via anaplerotic reactions using visible light, but instead utilizing ionizing radiation as a source of energy.[45]
Reproduction
Reproduction of fungi is complex, reflecting the heterogeneity in lifestyles and genetic makeup within this Kingdom of organisms.[46] Many reproduce either sexually or asexually, depending on conditions in the environment. These conditions trigger genetically determined developmental programs leading to the expression of specialized structures for sexual or asexual reproduction. These structures aid both reproduction and efficient dissemination of spores or spore-containing propagules.
Asexual reproduction
Asexual reproduction via vegetative spores or through mycelial fragmentation is common; it maintains clonal populations adapted to a specific niche, and allows more rapid dispersal than sexual reproduction.[47] In the case of the "Fungi imperfecti" or Deuteromycota, which lack a sexual cycle, it is the only means of propagation.
Sexual reproduction
Sexual reproduction with meiosis exists in all fungal phyla. It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and have been used to discriminate species based on morphological differences in sexual structures and reproductive strategies. Experimental crosses between fungal isolates can also be used to identify species based on biological species concepts. The major fungal groupings have initially been delineated based on the morphology of their sexual structures and spores; for example, the spore-containing structures, asci and basidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Species may possess vegetative incompatibility systems that allow mating only between individuals of opposite mating type, while others can mate and sexually reproduce with any other individual or itself. Species of the former mating system are called heterothallic, and of the latter homothallic.[48]
Most fungi have both a haploid and diploid stage in their life cycles. In sexually-reproducing fungi, compatible individuals combine by cell fusion of vegetative hyphae by anastomosis, required for the initiation of the sexual cycle. Ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from the two parents do not fuse immediately after cell fusion, but remain separate in the hyphal cells (see heterokaryosis).
In ascomycetes, dikaryotic hyphae of the hymenium form a characteristic hook at the hyphal septum. During cell division, formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. These asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. The ascospores are disseminated and germinate and may form a new haploid mycelium.[49]
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, formation of 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.[50] A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.[51] The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).
In zygomycetes, haploid hyphae of two individuals fuse, forming a gametangia, which develops into a zygospore. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which in turn may form asexual sporangiospores. These sporangiospores are means of rapid dispersal of the fungus and germinate into new genetically identical haploid fungal colonies, able to mate and undergo another sexual cycle followed by the generation of new zygospores, thus completing the lifecycle.[52]
Spore dispersal
Both asexual and sexual spores or sporangiospores are often actively dispersed by forcible ejection from their reproductive structures. This ejection ensures exit of the spores from the reproductive structures as well as travelling through the air over long distances.
Specialized mechanical and physiological mechanisms as well as spore-surface structures, such as hydrophobins, enable efficient spore ejection.[53] These mechanisms include, for example, forcible discharge of ascospores enabled by the structure of the ascus and accumulation of osmolytes in the fluids of the ascus that lead to explosive discharge of the ascospores into the air.[54] The forcible discharge of single spores termed ballistospores involves formation of a small drop of water (Buller's drop), which upon contact with the spore leads to its projectile release with an initial acceleration of more than 10,000 g.[55] Other fungi rely on alternative mechanisms for spore release, such as external mechanical forces, exemplified by puffballs. The bird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies.[56] Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.[57]
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.[58] The frequency and relative importance of parasexual events is unclear and may be lower than other sexual processes. However, it is known to play a role in intraspecific hybridization[59] and is also likely required for hybridization between species, which has been associated with major events in fungal evolution.[60]
Phylogeny and classification
For a long time, taxonomists considered fungi to be members of the Plant Kingdom; this was based mainly on similarities in lifestyle: both fungi and plants are mainly sessile, have similarities in general morphology and growth habitat (like plants, fungi often grow in soil, in the case of mushrooms forming conspicuous fruiting bodies, which sometimes bear resemblance to plants such as mosses). Moreover, both groups possess a cell wall, which is absent in the Animal Kingdom. However, 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.[61] Many studies have identified distinct morphological, biochemical, and genetic features in the Fungi, clearly delineating the fungi from the other kingdoms.
Physiological and morphological traits
Like animals and unlike most plants, fungi lack the capacity to synthesize organic carbon by chlorophyll-based photosynthesis; whereas plants store the reduced carbon as starch, fungi, like animals and some bacteria, use glycogen[62] for storage of carbohydrates. A major component of the cell wall in many fungal species is the nitrogen-containing carbohydrate, chitin,[63] also present in some animals, such as the insects and crustaceans, while the plant cell wall consists chiefly of the carbohydrate cellulose. The defining and unique characteristics of fungal cells include growth as hyphae, which are microscopic filaments between 2–10 µm in diameter and up to several centimeters in length, and which collectively form the mycelium. Some fungi, such as yeasts, grow as single cells, similar to unicellular algae and the protists.
Unlike many plants, most fungi lack an efficient vascular system, such as xylem or phloem for long-distance transport of water and nutrients. Some, such as Armillaria, form rhizomorphs or mycelial cords,[64] resembling and functionally related to, but morphologically distinct from plant roots.
Characteristics shared with plants include the presence of vacuoles in the cell,[10] and a similar pathway in the biosynthesis of terpenes using mevalonic acid and pyrophosphate as biochemical precursors; plants however use an additional terpene biosynthesis pathway in the chloroplasts that is apparently absent in fungi.[65] Ancestral traits shared among members of the fungi include chitinous cell walls and heterotrophy by absorption.[66] A further characteristic of the fungi that is absent from other eukaryotes, and shared only with some bacteria, is the biosynthesis of the amino acid L-lysine, via the α-aminoadipate metabolic pathway.[67]
Similar to plants, fungi produce a plethora of secondary metabolites functioning as defensive compounds or for niche adaptation; however, biochemical pathways for the synthesis of similar or even identical compounds often differ markedly between fungi and plants.[68][69] More than 60 species display the phenomenon of bioluminescence of mycelia or fruiting bodies.[70]
Evolutionary history
The first organisms which had features typical of fungi date back to the Proterozoic eon, some .[71] However, fungal fossils do not become common and uncontroversial until the early Devonian, when they are abundant in the Rhynie chert.[72]
Even though traditionally included in many botany curricula and textbooks, fungi are now thought to be more closely related to animals than to plants and are placed with the animals in the monophyletic group of opisthokonts.[73] For much of the Paleozoic Era, the fungi appear to have been aquatic, and consisted of organisms similar to the extant Chytrids in having flagellum-bearing spores.[74] The early fossil record of the fungi is meager. The fungi probably colonized the land during the Cambrian, long before land plants.[72] All modern classes of fungi were present in the Late Carboniferous (Pennsylvanian Epoch).[75] For some time after the Permian-Triassic extinction event, a fungal spike, originally thought to be an extraordinary abundance of fungal spores in sediments formed shortly after this event, suggested that they were the dominant life form at this time—nearly 100% of the fossil record available from this period.[76] However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess, [77] the spike did not appear worldwide,[78][79] and in many places it did not fall on the Permian-Triassic boundary.[80]
Analyses using molecular phylogenetics support a monophyletic origin of the Fungi.[26] The taxonomy of the Fungi is in a state of constant flux, especially due to recent research based on DNA comparisons. These current phylogenetic analyses often overturn classifications based on older and sometimes less discriminative methods based on morphological features and biological species concepts obtained from experimental matings.[81]
There is no unique generally accepted system at the higher taxonomic levels and there are frequent name changes at every level, from species upwards. However, efforts among researchers are now underway to establish and encourage usage of a unified and more consistent nomenclature.[26][82] Fungal species can also have multiple scientific names depending on its life cycle and mode (sexual or asexual) of reproduction. Web sites such as Index Fungorum and ITIS define preferred up-to-date names (with cross-references to older synonyms), but do not always agree with each other.
Taxonomic relationships
The current classification of Kingdom Fungi recognizes seven phyla,[26] two of which—the Ascomycota and the Basidiomycota—are contained within a branch representing subkingdom Dikarya. The below cladogram depicts the major fungal taxa and their relationship to opisthokont and unikont organisms. The lengths of the branches in this tree are not proportional to evolutionary distances.
| Unikonta |
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Taxonomic groups
The major divisions (phyla) of fungi have been classified based mainly on the characteristics of their sexual reproductive structures. Currently, seven divisions are proposed:[26]
Chytridiomycota
The Chytridiomycota are commonly known as chytrids. These fungi are ubiquitous with a worldwide distribution. Chytrids produce zoospores that are capable of active movement through aqueous phases with a single flagellum, leading early taxonomists to classify them as protists. Molecular phylogenies, inferred from rRNA sequences in ribosomes, suggest that the Chytrids are a basal group divergent from the other fungal divisions, consisting of four major clades with suggestive evidence for paraphyly or possibly polyphyly.[74]
Blastocladiomycota
The Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. Recent molecular data and ultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basiomycota). The blastocladiomycetes are fungi that are saprotrophs and parasites of all eukaryotic groups and undergo sporic meiosis unlike their close relatives, the chytrids, which mostly exhibit zygotic meiosis.[74]
Neocallimastigomycota
The Neocallimastigomycota were earlier placed in the phylum Chytridomycota. Members of this small phylum are anaerobic organisms, living in the digestive system of larger herbivorous mammals and possibly in other terrestrial and aquatic environments. They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.[26]
Zygomycota
The Zygomycota, commonly known as 'sugar' and 'pin' molds, reproduce sexually with meiospores called zygospores and asexually with sporangiospores. Black bread mold (Rhizopus stolonifer) is a common species that belongs to this group; another is Pilobolus species, capable of ejecting spores several meters through the air.[83] Medically relevant genera include Mucor, Rhizomucor, and Rhizopus. Molecular phylogenetic investigation has shown the Zygomycota to be a polyphyletic phylum with evidence of paraphyly within this taxonomic group.[84]
Glomeromycota
Members of the Glomeromycota form arbuscular mycorrhizae with higher plants. All known Glomeromycota species reproduce asexually.[85] The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago.[86]
Ascomycota
The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota. These fungi form meiotic spores called ascospores, which are enclosed in a special sac-like structure called an ascus. This division includes morels, a few mushrooms and truffles, single-celled yeasts (e.g., of the genera Saccharomyces, Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts. Prominent and important genera of filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), but analysis of molecular data has often been able to identify their closest teleomorphs in the Ascomycota. 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).
Basidiomycota
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, human commensal species of the genus Malassezia, and the opportunistic human pathogen, Cryptococcus neoformans.
Phylogenetic relationships with other organisms
Because of similarities in morphology and lifestyle, the slime molds (myxomycetes) and water molds (oomycetes) were formerly classified in the kingdom Fungi. Unlike true fungi, however, the cell walls of these organisms contain cellulose and lack chitin. Slime molds are unikonts like fungi, but are grouped in the Amoebozoa. Water molds are diploid bikonts, grouped in the Chromalveolate kingdom. Neither water molds nor slime molds are closely related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in mycology textbooks and primary research literature.
The nucleariids, currently grouped in the Choanozoa, may be a sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom.[87]
Ecology
Although often inconspicuous, fungi occur in every environment on Earth and play very important roles in most ecosystems. Along with bacteria, fungi are the major decomposers in most terrestrial (and some aquatic) ecosystems, and therefore play a critical role in biogeochemical cycles[88] and in many food webs. As decomposers, they play an indispensable 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.[89][90] Some individual fungal colonies can grow to a very large size and mass, in some cases reaching extraordinary dimensions and ages as in the case of a clonal colony of Armillaria ostoyae, which extends over an area of more than 900ha, with an estimated age of nearly 9,000 years.[91]
Symbiosis
Many fungi have important symbiotic relationships with organisms from most if not all Kingdoms.[92][93][94] 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.[95][96][97]
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.[98][99]
The mycorrhizal symbiosis is ancient, dating to at least 400 million years ago.[86] 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.[89][100] The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks".[101] Some species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.[102] 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.[103]
With algae and cyanobacteria
Lichens are formed by a symbiotic relationship between algae or cyanobacteria (referred to in lichen terminology as "photobionts") and fungi (mostly various species of ascomycetes and a few basidiomycetes), in which individual photobiont cells are embedded in a tissue formed by the fungus.[104] Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession, [105] and are the dominating life forms in extreme environments, including polar, alpine, and semiarid desert regions.[106] They are able to grow on different surfaces, including bare soil, rocks, tree bark, wood, shells or barnacles and leaves.[107] As in mycorrhizas, the photobiont provides sugars and other carbohydrates, while the fungus provides minerals and water. The functions of both symbiotic organisms are so closely intertwined that they function almost as a single organism; in most cases the resulting organism differs greatly from the individual components. Lichenization is a common mode of nutrition; around 20% of fungi—approximately 13,500 described species—are lichenized.[108] Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of dessication than most other photosynthetic organisms in the same habitat.[109]
With insects
Many insects also engage in mutualistic relationships with various types of fungi. Several groups of ants cultivate fungi in the order Agaricales as their primary food source, while ambrosia beetles cultivate various species of fungi in the bark of trees that they infest.[110] Similarly, females of several wood wasp species (genus Sirex) inject their eggs in addition to spores of the wood-rotting fungus Amylostereum areolatum; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae.[111] Termites on the African savannah are also known to cultivate fungi,[112] and yeasts of the genus Candida and Lachancea inhabit the gut of a wide range of different insects, including neuropterans, beetles, and cockroaches, but it is unknown if these fungi benefit their insect hosts.[113]
As pathogens and parasites
However, 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,[114] tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease,[115] and Cryphonectria parasitica responsible for chestnut blight,[116] and plant pathogens in the genera Fusarium, Ustilago, Alternaria, and Cochliobolus.[96] Certain fungi, like Paecilomyces lilacinus, are predators of nematodes, which they capture using an array of specialized structures such as constricting rings or adhesive nets.[117]
Some fungi can cause serious diseases in humans, several of which may be fatal if untreated. These include aspergilloses, candidoses, coccidioidomycosis, cryptococcosis, histoplasmosis, mycetomas, and paracoccidioidomycosis. Furthermore, persons with immuno-deficiencies are particularly susceptible to disease by genera such as Aspergillus, Candida, Cryptoccocus,[97][118][119] Histoplasma,[120] and Pneumocystis.[121] Other fungi can attack eyes, nails, hair, and especially skin, the so-called dermatophytic and keratinophilic fungi,[122] and cause local infections such as ringworm and athlete’s foot. Fungal spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic reactions.[123]
Human use
Human use of fungi for food preparation or preservation and other purposes is extensive and has a long history: yeasts are required for fermentation of beer, wine and bread, other fungal species are used in the production of soy sauce and tempeh. Mushroom farming and mushroom gathering are large industries in many countries. Many species produce antibiotics, including β-lactam antibiotics such as penicillin and cephalosporin.[124] Widespread use of these antibiotics for the treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and many others began in the early 20th century and continues to play a major part in anti-bacterial chemotherapy. The study of the historical uses and sociological impact of fungi is known as ethnomycology.
Cultured foods
Baker's yeast or Saccharomyces cerevisiae, a single-cell fungus, is used to bake bread and other wheat-based products, such as pizza and dumplings.[125] Yeast species of the genus Saccharomyces are also used to produce alcoholic beverages through fermentation.[126] Mycelial fungi, such as the shoyu koji mold (Aspergillus oryzae), are used to brew Shoyu (soy sauce), and to prepare tempeh.[127] Quorn is a high-protein product made from the mold Fusarium venenatum, and is used in vegetarian cooking.[128]
Medicinal use
 |  | |
| The medicinal fungi Ganoderma lucidum (left) and Cordyceps sinensis (right). | ||
Certain mushrooms enjoy usage as therapeutics in traditional and folk medicines, such as Traditional Chinese Medicine. Most notable species include those of the genus Agaricus,[129][130] Ganoderma,[131] and Cordyceps,[132] which are being used in the treatment of several diseases.[133] Research has identified compounds produced by these fungi that have biological effects against viruses[134][135] and cancer cells in vitro;[136] specific metabolites with biological or antimicrobial activities, such as 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.[137][138] In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from Trametes versicolor, is an approved adjuvant for cancer therapy.[139]
Edible and poisonous species
Well-known types of fungi are the edible and the poisonous mushrooms. Many species are commercially raised, but others must be harvested from the wild. Agaricus bisporus, sold as button mushrooms when small or Portobello mushrooms when larger, are a commonly-eaten species, used in salads, soups, and many other dishes. Many Asian fungi are commercially grown and have gained in popularity in the West. They are often available fresh in grocery stores and markets, including straw mushrooms (Volvariella volvacea), oyster mushrooms (Pleurotus ostreatus), shiitakes (Lentinula edodes), and enokitake (Flammulina spp.).
There are many more mushroom species that are harvested from the wild for personal consumption or commercial sale. Milk mushrooms, morels, chanterelles, truffles, black trumpets, and porcini mushrooms (Boletus edulis) (also known as king boletes) demand a high price on the market. They are often used in gourmet dishes.
For certain types of cheeses, it is also a common practice to inoculate milk curds with fungal spores to promote the growth of specific species of mold that impart a unique flavor and texture to the cheese. This accounts for the blue color in cheeses such as Stilton or Roquefort which is created using Penicillium roqueforti spores.[140] Molds used in cheese production are usually non-toxic and are thus safe for human consumption; however, mycotoxins (e.g., aflatoxins, roquefortine C, patulin, or others) may accumulate due to spoilage during cheese ripening or storage.[141]
Many mushroom species are toxic to humans, with toxicities ranging from slight digestive problems or allergic reactions as well as hallucinations to severe organ failures and death. The most deadly mushrooms belong to the genera Inocybe, Cortinarius, and most infamously, Amanita. The latter genus includes the destroying angel (A. virosa) and the death cap (A. phalloides), the most common cause of deadly mushroom poisoning.[142] The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.[143] Tricholoma equestre was considered edible until being implicated in serious poisonings causing rhabdomyolysis.[144]
Fly agaric mushrooms (Amanita muscaria) also cause occasional poisonings, mostly as a result of ingestion for use as a recreational drug for its hallucinogenic properties. Historically, fly agaric was used by Celtic Druids in Northern Europe and the Koryak people of north-eastern Siberia for religious or shamanic purposes.[145] Because it is difficult to accurately identify a safe mushroom without proper training and knowledge, it is often advised to assume that a mushroom in the wild is poisonous and not to consume it.[146][147]
In the biological control of pests
In agriculture, fungi that actively compete for nutrients and space with pathogenic microorganisms such as bacteria or other fungi, via the competitive exclusion principle,[148] or are parasites of these pathogens, may be beneficial agents for human use. For example, certain species may be used to suppress growth or eliminate harmful plant pathogens, such as insects, mites, weeds, nematodes and other fungi that cause diseases of important crop plants.[149] This has generated strong interest in the use and practical application of these fungi for the biological control of these agricultural pests. Entomopathogenic fungi can be used as biopesticides, as they actively kill insects.[150] Examples that have been used as biological insecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella spp, Paecilomyces spp, and Verticillium lecanii.[151][152] Endophytic fungi of grasses of the genus Neotyphodium, such as N. coenophialum, produce alkaloids that are toxic to a range of invertebrate and vertebrate herbivores. These alkaloids protect grass plants from herbivory, but several endophyte alkaloids can poison grazing animals, such as cattle and sheep.[153] Infecting cultivars of pasture or forage grasses with Neotyphodium endophytes is one approach being used in grass breeding programs; the fungal strains are selected for producing only alkaloids that increase resistance to herbivores such as insects, while being non-toxic to livestock.[154]
Bioremediation
Certain fungi, in particular 'white rot' fungi, can degrade insecticides, herbicides, pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, water, and basic elements.[155] Fungi have been shown to biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.[156][157][158]
Others
Fungi are used extensively to produce industrial chemicals like citric, gluconic, lactic, and malic acids, antibiotics, and even to make stonewashed jeans.[159] Fungi are also sources of industrial enzymes, such as lipases used in biological detergents,[160] amylases,[161] cellulases,[162] invertases, proteases and xylanases.[163] Several species, most notably Psilocybin mushrooms (colloquially known as magic mushrooms), are ingested for their psychedelic properties, both recreationally and religiously.
Mycotoxins
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 those mycotoxins that are produced by molds causing food spoilage and poisonous mushrooms (see above). Particularly infamous are the aflatoxins, which are insidious liver toxins and highly carcinogenic metabolites produced by Aspergillus species often growing in or on grains and nuts consumed by humans, ergot alkaloids produced by Claviceps species, which cause ergotism (e.g, St Anthony's Fire) with a long history of serious epidemic outbreaks occurring in people consuming rye or related cereals contaminated with sclerotia of the ergot fungus, Claviceps purpurea,[164] and the lethal amatoxins produced by mushrooms of the genus Amanita. Other notable mycotoxins include ochratoxins, patulin, and trichothecenes (e.g., T-2 mycotoxin) and fumonisins, which have significant impact on human food supplies or animal livestock.[165]
Mycotoxins belong to the group of secondary metabolites (or natural products). Recent research has shown the existence of biochemical pathways solely for the purpose of producing mycotoxins and other natural products in fungi.[166] Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory).[167][168] These fitness benefits and the existence of dedicated biosynthetic pathways for mycotoxin production suggest that the mycotoxins are important for persistence and survival.
Mycology
Mycology is the branch of biology concerned with the systematic study of fungi, including their genetic and biochemical properties, their taxonomy, and their use to humans as a source of medicine, food, entheogens, as well as their dangers, such as poisoning or infection. The field of phytopathology, the study of plant diseases, is closely related because most plant pathogens are fungi.
Man's dealings with fungi date 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).[169] Ancient peoples have used fungi as food sources – often unknowingly – for millennia, in the preparation of leavened bread and fermented juices. Man's oldest written records contain references to the destruction of crops that were probably caused by pathogenic fungi.[170]
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