Fungus

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For the fictional character, see Fungus the Bogeyman. For the music genre, see Fungi (music)

Fungi (singular fungus) are a kingdom of eukaryotic organisms. The fungi are heterotrophic organisms characterized by a chitinous cell wall, and in the majority of species, filamentous growth as multicellular hyphae forming a mycelium; some fungal species also grow as single cells. Sexual and asexual reproduction is via spores, often produced on specialized structures or in fruiting bodies. Yeasts, molds, and mushrooms are examples of fungi. The discipline of biology devoted to the study of fungi is known as mycology.

[edit] General features and distribution

The Fungi have a worldwide distribution, and grow in a wide range of habitats, including deserts. Most fungi grow in terrestrial environments, but several species occur only in aquatic habitats. Fungi along with bacteria are the primary decomposers of organic matter in almost all terrestrial ecosystems worldwide. There are an estimated 1.5 million fungal species of which around 70,000 have been described. Most fungi grow as thread-like filaments called hyphae, which form a mycelium, while others grow as single cells. ^[2][3]

[edit] Importance for 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 ^[4] and bread, some other fungal species are used in the production of soy sauce and tempeh, and mushroom farming and gathering is a large industry in many countries. Many fungi are producers of antibiotics, including β-lactam antibiotics such as penicillin and cephalosporin.^[5] 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.

[edit] Cultured foods

Baker's yeast or Saccharomyces cerevisiae, a single-cell fungus, is used in the baking of bread and other wheat-based products, such as pizza and dumplings.^[6] Several yeast species of the genus Saccharomyces are also used in the production of alcoholic beverages through fermentation.^[7] Mycelial fungi, such as the shoyu koji mold (Aspergillus oryzae), are used in the brewing of Shoyu (soy sauce) and preparation of tempeh.^[8] Quorn is a high-protein product made from the mould, Fusarium venenatum, and is used in vegetarian cooking.

[edit] Other human uses

Fungi are also used extensively to produce industrial chemicals like lactic acid, antibiotics and even to make stonewashed jeans.^[9] Several fungal species are ingested for their psychedelic properties, both recreationally and religiously (see main article, Psilocybin mushrooms).

[edit] Edible and poisonous fungi

Some of the most well-known types of fungi are the edible and 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 musrooms when larger, are the most commonly eaten species, used in salads, soups, and many other dishes. Other commercially grown mushrooms that have gained in popularity in the West and are often available fresh in grocery stores include 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 (also known as king boletes) all 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 foment the growth of specific species of mold that impart a unique flavor and texture to the cheese. This accounts for the blue colour in cheeses such as Stilton or Roquefort which is created using Penicillium roqueforti spores.^[10] Molds used in cheese production are usually non-toxic and are thus safe for human consumption; however, toxic fungal metabolites (e.g., aflatoxins, roquefortine C, patulin, or others) may accumulate due to fungal spoilage during cheese ripening or storage.^[11]

Many mushroom species are toxic to humans, with toxicities ranging from slight digestive problems or allergic reactions as well as hallucination to severe organ failures and death. Some of the most deadly mushrooms belong to the genera Inocybe, Cortinarius, and most infamously, Amanita, which includes the destroying angel (A. virosa) and the death cap (A. phalloides), the most common cause of deadly mushroom poisoning. ^[12] Fly agaric mushrooms (A. 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.^[13] It is difficult to identify a safe mushroom without proper training and knowledge, thus it is often advised to assume that a mushroom in the wild is poisonous and not to consume it.

[edit] Fungi in the biological control of pests

Some fungi capable of competing with or infecting other organisms are considered beneficial for human use. For example in agriculture, some fungi may be used to restrict or eliminate the populations of harmful organisms like pest insects, mites, weeds, nematodes and other fungi, such as those that affect the growth or even kill plants.^[14] This has generated strong interest in the use and practical application of these fungi for the biological control of pests. Some of these fungi can be used as biopesticides, like the ones that kill insects (entomopathogenic fungi).^[15] Specific examples of fungi that have been developed as bioinsecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella, Paecilomyces fumosoroseus, and Verticillium lecanii.^{[16] [17]} Endophytic fungi of grasses of the genus Neotyphodium, such as N. coenophialum produce alkaloids toxic to a range of different herbivores, thus protecting the grass plants from herbivory, but also causing poisoning of grazing animals, such as cattle and sheep. ^[18] Infection of grass cultivars of turf or forage grasses with isolates of the grass endophytes that produce only specific alkaloids to improve grass hardiness and resistance to herbivores such as insects, while being non-toxic to livestock, is being used in grass breeding programs.^[19]

[edit] Ecological role

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 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.^[20][21]

[edit] Fungi as symbionts

Many fungi have important symbiotic relationships with organisms from most if not all Kingdoms.^[22][23][24] These interactions can be mutualistic or antagonistic in nature, or in case of commensal fungi are of no apparent benefit or detriment to the host. ^[25][26][27]

[edit] In symbiosis 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 some kind of mycorrhizal relationship with fungi and are dependent upon this relationship for survival.^[28][29][30] The mycorrhizal symbiosis is ancient, dating to at least 400 million years ago.^[31] 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.^[20] In some mycorrhizal associations, the fungal partners may mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks". ^[32]

Lichens are formed by a symbiotic relationship between algae or cyanobacteria (referred to in lichens 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. ^{[citation needed]} 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. ^{[citation needed]}

[edit] In symbiosis 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.^[33] Termites on the African Savannah are also known to cultivate fungi.^[34]

[edit] Fungi as pathogens and parasites

However, many fungi are parasites on plants, animals (including humans), and other fungi. Serious fungal pathogens of many cultivated plants causing extensive damage and losses to agriculture and forestry include the rice blast fungus Magnaporthe grisea,^[35] tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease,^[36] and Cryphonectria parasitica responsible for chestnut blight, ^[37] and plant-pathogenic fungi in the genera Fusarium, Ustilago, Alternaria, and Cochliobolus; ^[26] fungi with the potential to cause serious human diseases, especially in persons with immuno-deficiencies, are in the genera Aspergillus, Candida, Cryptoccocus,^[38][27][39] Histoplasma,^[40] and Pneumocystis. ^[41] Several pathogenic fungi are also responsible for relatively minor human diseases, such as athlete’s foot and ringworm. Some fungi are predators of nematodes, which they capture using an array of devices such as constricting rings or adhesive nets.^[42]

[edit] Nutrition and possible autotrophy in fungi

Growth of fungi as 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. 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. ^[43][44][45] These molecules are then absorbed as nutrients into the fungal cells.

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 many of them to use a large variety of organic substrates for growth, including simple compounds as nitrate, ammonia, acetate, or ethanol.^{[46] [47]} Recent research raises the possibility that some fungi utilize the pigment melanin to extract energy from ionizing radiation, such as gamma radiation for "radiotrophic" growth. ^[48] It has been proposed that this process might bear some similarity to photosynthesis in plants, ^[48] but detailed biochemical data supporting the existence of this hypothetical pathway are presently lacking.

[edit] Morphology

Though fungi are part of the opisthokont clade, all phyla except for the chytrids have lost their posterior flagella.^[49] 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.^[50] Many fungi grow as thread-like filamentous macroscopic structures called hyphae, and an assemblage of intertwined and interconnected hyphae is called a mycelium. ^[2] 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 (see figure), and are commonly and generically called mould; fungal mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies, with many species exhibiting characteristic macroscopic growth morphologies and colours, due to spores or pigmentation.

Hyphae can be septate, i.e., divided into hyphal compartments separated by a septum, each compartment containing one or more nuclei or can be coenocytic, i.e., lacking hyphal compartmentalization. However, septa have pores, such as the doliporus in the basidiomycetes that allow cytoplasm, organelles, and sometimes nuclei to pass through.^[2] Coenocytic hyphae are essentially multinucleate supercells. ^{[citation needed]} In some cases, fungi have developed specialized structures for nutrient uptake from living hosts; examples include haustoria in plant-parasitic fungi of nearly all divisions, and arbuscules of several mycorrhizal fungi ^[51], which penetrate into the host cells for nutrient uptake by the fungus. Specialized fungal structures important in sexual reproduction are the apothecia, perithecia, and cleistothecia in the ascomycetes, and the fruiting bodies of the basidiomycetes, and a few ascomycetes, which can sometimes grow very large and are well known as mushrooms.

[edit] Reproduction

Reproduction of fungi is complex, reflecting the heterogeneity in lifestyles and genetic make up within this group of organisms. ^[2] Many fungi reproduce both 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.

[edit] Asexual reproduction

Asexual reproduction via vegetative spores or through mycelial fragmentation is common in many fungal species and allows more rapid dispersal than sexual reproduction. In the case of the "Fungi imperfecti" or Deuteromycota, which lack a sexual cycle, it is the only means of propagation. Asexual spores, upon germination, may found a population that is clonal to the population from which the spore originated, and thus colonize new environments.

[edit] Sexual reproduction

Sexual reproduction with meiosis exists in all fungal phyla, except the Deuteromycota. It differs in many aspects from sexual reproduction in animals or plants. Many differences also exist between fungal groups and have been used to discriminate fungal clades and 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 clades 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. Many fungal species have elaborate 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. ^[52]

Most fungi have both a haploid and diploid stage in their life cycles. In all 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 fungi, dikaryotic hyphae form asci (sing. ascus), in which karyogamy (nuclear fusion) occurs. These asci are embedded in an ascocarp, or fruiting body, of the fungus. 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.

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, in many cases also present in the vegetatively growing mycelium. A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.^[53] The most commonly known basidiocarps are mushrooms, but they may also take many other forms (see Morphology section).

In zygomycetes, haploid hyphae of two individuals fuse, forming a zygote, which develops into a zygospore. When the zygospore germinates, it quickly 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.

[edit] Other sexual processes

Besides regular sexual reproduction with meiosis, some fungal species may exchange genetic material via parasexual processes, initiated by anastomosis between hyphae and plasmogamy of fungal cells. 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 ^[54] and is also likely required for hybridization between fungal species, which has been associated with major events in fungal evolution. ^[55]

[edit] Phylogeny and classification

For a long time taxonomists considered fungi to be members of the Plant Kingdom. This early classification was based mainly on similarities in lifestyle: both fungi and plant 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 approximately one billion years ago.^[56] Many studies have identified several distinct morphological, biochemical, and genetic features in the Fungi, clearly delineating this group from the other kingdoms. For these reasons, the fungi are placed in their own kingdom, Eumycota.

[edit] Physiological and morphological traits

Similar to 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 ^[57] for storage of carbohydrates. A major component of the cell wall in many fungal species is the nitrogen-containing carbohydrate, chitin,^[58] 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 of between 2-10 microns in diameter and up to several centimetres in length, and which combined form the fungal mycelium. Some fungi, such as yeasts, grow as single ovoid 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; as an example for convergent evolution, some fungi, such as Armillaria, form rhizomorphs or mycelial cords,^[59] resembling and functionally related to, but morphologically distinct from, plant roots.

Some characteristics shared between plants and fungi include the presence of vacuoles in the cell ^[60], 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.^[61] Ancestral traits shared among members of the fungi include chitinous cell walls and heterotrophy by absorption.^[62] 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 pathway. ^[63]

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. ^[64][65]

[edit] Evolutionary history

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. ^[62]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.^[66] The first land fungi probably appeared in the Silurian, right after the first land plants appeared, even though their fossils are fragmentary. For some time after the Permian-Triassic extinction event, a fungal spike, detected as an extraordinary abundance of fungal spores in sediments formed shortly after this event, indicates that they were the dominant life form during this period—nearly 100% of the fossil record available from this period.^[67]

Analyses using molecular phylogenetics support a monophyletic origin of the the Fungi.^[68] 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.^[69][70]

There is no unique generally accepted system at the higher taxonomic levels and there are constant name changes at every level, from species upwards. However, efforts among fungal researchers are now underway to establish and encourage usage of a unified and more consistent nomenclature.^[68] 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.

[edit] Cladogram

[edit] The taxonomic groups of fungi

The major divisions (phyla) of fungi have been classified based mainly on their sexual reproductive structures. Currently, seven fungal divisions are proposed:^[68]

• 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. Consequently, some taxonomists had earlier classified them as protists on the basis of the flagellum. Molecular phylogenies, inferred from the rRNA-operon sequences representing the 18S, 28S, and 5.8S ribosomal subunits, suggest that the Chytrids are a basal fungal group divergent from the other fungal divisions, consisting of four major clades with some evidence for paraphyly or possibly polyphyly. ^[66]
• 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. ^[66]
• 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.^[68]
• The Zygomycota contain the taxa, Zygomycetes and Trichomycetes, and 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, which is capable of ejecting spores several meters through the air. 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. ^[71]
• Members of the Glomeromycota are fungi forming arbuscular mycorrhizae with higher plants. Only one species has been observed forming zygospores; all other species solely reproduce asexually. The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago.^[31]

• 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 ascomycetes species have only been observed undergoing asexual reproduction (called anamorphic species), but 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, several ascomyctes have been used for elucidating principles of genetics and heredity (e.g. Neurospora crassa).
• 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 (fungus) and smut fungi, which are major pathogens of grains. Other important Basidiomyces include the maize pathogen,Ustilago maydis, human commensal species of the genus Malassezia, and the opportunistic human pathogen, Cryptococcus neoformans.

[edit] Phylogenetic relationships with other fungus-like organisms

Although the water molds or oomycetes and slime molds or myxomycetes have traditionally been placed in the kingdom Fungi and those who study them are still called mycologists, they are not true fungi. Unlike true fungi, the cell walls of water molds and slime molds contain cellulose and lack the carbohydrate-polymer, chitin, and many of the oomycetes are diploid organisms. Slime molds are unikonts like fungi, but are grouped in the Amoebozoa. Water molds, however, are bikonts, grouped in the Chromalveolate kingdom.