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Fungus
A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as
yeasts and molds, as well as the more familiar mushrooms.
These organisms are classified as a kingdom, Fungi, which is separate
from the other eukaryotic life kingdoms of plants and animals.
A characteristic that places fungi in a different kingdom from plants, bacteria,
and some protists is chitin in their cell walls. Similar to animals, fungi are heterotrophs;
they acquire their food by absorbing dissolved molecules, typically
by secreting digestive enzymes into their environment. Fungi do not photosynthesise.
Growth is their means of mobility, except for spores, which may travel through the air or water.
Fungi are the principal decomposers in ecological systems. These
and other differences place fungi in a single group of related organisms, named the Eumycota,
which share a common ancestor, an interpretation that is also strongly supported
by molecular phylogenetics. This fungal group is distinct
from the structurally similar myxomycetes and oomycetes. The discipline of biology devoted
to the study of fungi is known as mycology. In the past,
mycology was regarded as a branch of botany,
although it is now known fungi are genetically more closely related to animals than to plants.
Abundant worldwide, most fungi are inconspicuous, because of the small size of their structures,
and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals,
or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms
or as molds. Fungi perform an essential role in the decomposition of organic matter
and have fundamental roles in nutrient cycling and exchange in the environment.
They have long been used as a direct source of human food, in the form of mushrooms and truffles;
as a leavening agent for bread; and in the fermentation of various food products, such as wine,
beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and,
more recently, various enzymes produced by fungi are used industrially and in detergents.
Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests.
Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides,
that are toxic to animals including humans.
The fruiting structures of a few species contain psychotropic compounds
and are consumed recreationally or in traditional spiritual ceremonies.
Fungi can break down manufactured materials and buildings,
and become significant pathogens of humans and other animals. Losses of crops due
to fungal diseases or food spoilage can have a large impact on human food supplies
and local economies. The fungus kingdom encompasses an enormous diversity of taxa
with varied ecologies, life cycle strategies, and morphologies ranging
from unicellular aquatic chytrids to large mushrooms. However,
little is known of the true biodiversity of Kingdom Fungi, which has been estimated
at 1.5 million to 5 million species,
with about 5% of these having been formally classified. Ever since the pioneering 18th
and 19th century taxonomical works of Carl Linnaeus, Christian Hendrik Persoon,
and Elias Magnus Fries, fungi have been classified according to their morphology or physiology.
Advances in molecular genetics have opened the way for DNA analysis
to be incorporated into taxonomy,
which has sometimes challenged the historical groupings based on morphology and other traits.
Phylogenetic studies published in the last decade have helped reshape the classification within
Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla.
 Etymology 
The English word fungus is directly adopted from the Latin fungus,
used in the writings of Horace and Pliny. This in turn is derived from the Greek word sphongos,
which refers to the macroscopic structures and morphology of mushrooms and molds;
the root is also used in other languages, such as the German Schwamm and Schimmel.
The use of the word mycology, which is derived from the Greek mykes and logos,
to denote the scientific study of fungi is thought to have originated in 1836
with English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward
Smith, Vol. 5. A group of all the fungi present in a particular area
or geographic region is known as mycobiota, and more, "the mycobiota of Ireland".
 Characteristics 
 [^]  Before the introduction of molecular methods for phylogenetic analysis,
taxonomists considered fungi to be members of the plant kingdom,
because of similarities in lifestyle: both fungi and plants are mainly immobile,
and have similarities in general morphology and growth habitat. Like plants,
fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit bodies,
which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom,
distinct from both plants and animals, from which they appear
to have diverged around one billion years ago. Some morphological, biochemical,
and genetic features are shared with other organisms, while others are unique to the fungi,
clearly separating them
from the other kingdoms: Shared features: Unique features:  [^]  Most fungi lack an efficient system
for the long-distance transport of water and nutrients, such as the xylem
and phloem in many plants. To overcome this limitation, some fungi, such as Armillaria,
form rhizomorphs, which resemble and perform functions similar to the roots of plants.
As eukaryotes, fungi possess a biosynthetic pathway for producing terpenes that uses mevalonic acid
and pyrophosphate as chemical building blocks. Plants
and some other organisms have an additional terpene biosynthesis pathway in their chloroplasts,
a structure fungi and animals do not have.
Fungi produce several secondary metabolites that are similar or identical in structure
to those made by plants. Many of the plant and fungal enzymes that make these compounds differ
from each other in sequence and other characteristics, which indicates separate origins
and convergent evolution of these enzymes in the fungi and plants.
 Diversity 
 [^]  Fungi have a worldwide distribution, and grow in a wide range of habitats,
including extreme environments such as deserts or areas with high salt concentrations
or ionizing radiation, as well as in deep sea sediments. Some can survive the intense UV
and cosmic radiation encountered during space travel. Most grow in terrestrial environments,
though several species live partly or solely in aquatic habitats,
such as the chytrid fungus Batrachochytrium dendrobatidis, a parasite that has been responsible
for a worldwide decline in amphibian populations.
This organism spends part of its life cycle as a motile zoospore, enabling it
to propel itself through water and enter its amphibian host.
Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.
Around 100,000 species of fungi have been formally described by taxonomists,
but the global biodiversity of the fungus kingdom is not fully understood.
On the basis of observations of the ratio of the number of fungal species
to the number of plant species in selected environments, the fungal kingdom has been estimated
to contain about 1.5 million species. A recent estimate suggests there may be
over 5 million species. In mycology, species have historically been distinguished
by a variety of methods and concepts. Classification based on morphological characteristics,
such as the size and shape of spores or fruiting structures,
has traditionally dominated fungal taxonomy. Species may also be distinguished by their biochemical
and physiological characteristics, such as their ability to metabolize certain biochemicals,
or their reaction to chemical tests.
The biological species concept discriminates species based on their ability to mate.
The application of molecular tools, such as DNA sequencing and phylogenetic analysis,
to study diversity has greatly enhanced the resolution and added robustness
to estimates of genetic diversity within various taxonomic groups.  [^]  Fungi has 36,000
or more sexes; most species have only two sexes.
 Mycology 
Mycology is the branch of biology concerned with the systematic study of fungi,
including their genetic and biochemical properties, their taxonomy, and their use
to humans as a source of medicine, food, and psychotropic substances consumed
for religious purposes, as well as their dangers, such as poisoning or infection.
The field of phytopathology, the study of plant diseases, is closely related,
because many plant pathogens are fungi.  [^]  The use of fungi by humans dates back to prehistory;
Ötzi the Iceman,
a well-preserved mummy of a 5,300-year-old Neolithic man found frozen in the Austrian Alps,
carried two species of polypore mushrooms that may have been used as tinder, or
for medicinal purposes.
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.
 History 
Mycology is a relatively new science that became systematic after the development of the
microscope in the 17th century. Although fungal spores were first observed
by Giambattista della Porta in 1588, the seminal work in the development of mycology is considered
to be the publication of Pier Antonio Micheli's 1729 work Nova plantarum genera.
Micheli not only observed spores, but also showed that, under the proper conditions,
they could be induced into growing into the same species of fungi from which they originated.
Extending the use of the binomial system of nomenclature introduced
by Carl Linnaeus in his Species plantarum,
the Dutch Christian Hendrik Persoon established the first classification of mushrooms
with such skill so as to be considered a founder of modern mycology. Later,
Elias Magnus Fries further elaborated the classification of fungi, using spore color
and various microscopic characteristics, methods still used by taxonomists today.
Other notable early contributors to mycology in the 17th–19th
and early 20th centuries include Miles Joseph Berkeley, August Carl Joseph Corda, Anton de Bary,
the brothers Louis René and Charles Tulasne, Arthur H. R. Buller, Curtis G. Lloyd,
and Pier Andrea Saccardo. The 20th century has seen a modernization of mycology that has come
from advances in biochemistry, genetics, molecular biology, and biotechnology.
The use of DNA sequencing technologies
and phylogenetic analysis has provided new insights into fungal relationships and biodiversity,
and has challenged traditional morphology-based groupings in fungal taxonomy.
 Microscopic structures 
 [^]  Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10 µm in diameter
and up to several centimeters in length. Hyphae grow at their tips ;
new hyphae are typically formed by emergence of new tips along existing hyphae
by a process called branching, or occasionally growing hyphal tips fork, giving rise
to two parallel-growing hyphae. Hyphae also sometimes fuse when they come into contact,
a process called hyphal fusion. These growth processes lead to the development of a mycelium,
an interconnected network of hyphae. Hyphae can be either septate or coenocytic.
Septate hyphae are divided into compartments separated by cross walls,
with each compartment containing one or more nuclei; coenocytic hyphae are not compartmentalized.
Septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through;
an example is the dolipore septum in fungi of the phylum Basidiomycota.
Coenocytic hyphae are in essence multinucleate supercells.
Many species have developed specialized hyphal structures for nutrient uptake from living hosts;
examples include haustoria in plant-parasitic species of most fungal phyla,
and arbuscules of several mycorrhizal fungi, which penetrate into the host cells
to consume nutrients.
Although fungi are opisthokonts—a grouping of evolutionarily related organisms broadly
characterized by a single posterior flagellum—all phyla except
for the chytrids have lost their posterior flagella.
Fungi are unusual among the eukaryotes in having a cell wall that, in addition to glucans
and other typical components, also contains the biopolymer chitin.
 Macroscopic structures 
 [^]  Fungal mycelia can become visible to the naked eye, for example, on various surfaces
and substrates, such as damp walls and spoiled food, where they are commonly called molds.
Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies.
These colonies can exhibit growth shapes
and colors that can be used as diagnostic features in the identification of species or groups.
Some individual fungal colonies can reach extraordinary dimensions
and ages as in the case of a clonal colony of Armillaria solidipes, which extends
over an area of more than 900 ha, with an estimated age of nearly 9,000 years.
The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a
cup-shaped fruit body that is often macroscopic and holds the hymenium,
a layer of tissue containing the spore-bearing cells. The fruit bodies of the basidiomycetes
and some ascomycetes can sometimes grow very large, and many are well known as mushrooms.
 Growth and physiology 
 [^]  The growth of fungi as hyphae on or in solid substrates
or as single cells in aquatic environments is adapted for the efficient extraction of nutrients,
because these growth forms have high surface area to volume ratios. Hyphae are specifically adapted
for growth on solid surfaces, and to invade substrates and tissues.
They can exert large penetrative mechanical forces; for example, many plant pathogens,
including Magnaporthe grisea, form a structure called an appressorium that evolved
to puncture plant tissues. The pressure generated by the appressorium,
directed against the plant epidermis, can exceed.
The filamentous fungus Paecilomyces lilacinus uses a similar structure
to penetrate the eggs of nematodes. The mechanical pressure exerted
by the appressorium is generated from physiological processes that increase intracellular turgor
by producing osmolytes such as glycerol. Adaptations such as these are complemented
by hydrolytic enzymes secreted into the environment
to digest large organic molecules—such as polysaccharides, proteins,
and lipids—into smaller molecules that may then be absorbed as nutrients.
The vast majority of filamentous fungi grow in a polar fashion by elongation
at the tip of the hypha.
Other forms of fungal growth include intercalary extension as in the case of some endophytic fungi,
or growth by volume expansion during the development of mushroom stipes and other large organs.
Growth of fungi as multicellular structures consisting of somatic
and reproductive cells—a feature independently evolved in animals
and plants—has several functions, including the development of fruit bodies
for dissemination of sexual spores and biofilms for substrate colonization
and intercellular communication. The fungi are traditionally considered heterotrophs,
organisms that rely solely on carbon fixed by other organisms for metabolism.
Fungi have evolved a high degree of metabolic versatility that allows them
to use a diverse range of organic substrates for growth,
including simple compounds such as nitrate, ammonia, acetate, or ethanol.
In some species the pigment melanin may play a role in extracting energy from ionizing radiation,
such as gamma radiation. This form of "radiotrophic" growth has been described
for only a few species, the effects on growth rates are small, and the underlying biophysical
and biochemical processes are not well known. This process might bear similarity
to CO2 fixation via visible light, but instead uses ionizing radiation as a source of energy.
 Reproduction 
 [^]  Fungal reproduction is complex, reflecting the differences in lifestyles
and genetic makeup within this diverse kingdom of organisms.
It is estimated that a third of all fungi reproduce using more than one method of propagation;
for example,
reproduction may occur in two well-differentiated stages within the life cycle of a species,
the teleomorph and the anamorph.
Environmental conditions trigger genetically determined developmental states that lead
to the creation of specialized structures for sexual or asexual reproduction.
These structures aid reproduction by efficiently dispersing spores or spore-containing propagules.
 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 traveling through the air
over long distances. [^]  Specialized mechanical and physiological mechanisms,
as well as spore surface structures, enable efficient spore ejection. For example,
the structure of the spore-bearing cells in some ascomycete species is such that the buildup of
substances affecting cell volume
and fluid balance enables the explosive discharge of spores into the air.
The forcible discharge of single spores termed ballistospores involves formation of a small drop of
water, which upon contact with the spore leads to its projectile release
with an initial acceleration of more than 10,000 g;
the net result is that the spore is ejected 0.01–0.02 cm, sufficient distance for it
to fall through the gills or pores into the air below. Other fungi, like the puffballs,
rely on alternative mechanisms for spore release, such as external mechanical forces.
The bird's nest fungi use the force of falling water drops to liberate the spores
from cup-shaped fruiting bodies. Another strategy is seen in the stinkhorns, a group of fungi
with lively colors and putrid odor that attract insects to disperse their spores.
 Evolution 
In contrast to plants and animals, the early fossil record of the fungi is meager.
Factors that likely contribute
to the under-representation of fungal species among fossils include the nature of fungal fruiting
bodies, which are soft, fleshy, and easily degradable tissues
and the microscopic dimensions of most fungal structures,
which therefore are not readily evident. Fungal fossils are difficult to distinguish
from those of other microbes, and are most easily identified when they resemble extant fungi.
Often recovered from a permineralized plant or animal host, these samples are typically studied
by making thin-section preparations that can be examined with light microscopy
or transmission electron microscopy. Researchers study compression fossils
by dissolving the surrounding matrix with acid and then using light
or scanning electron microscopy to examine surface details.
The earliest fossils possessing features typical of fungi date to the Paleoproterozoic era,
some ; these multicellular benthic organisms had filamentous structures capable of anastomosis.
Other studies estimate the arrival of fungal organisms
at about 760–1060 Ma on the basis of comparisons of the rate of evolution in closely related
groups. 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.
The evolutionary adaptation from an aquatic
to a terrestrial lifestyle necessitated a diversification of ecological strategies
for obtaining nutrients, including parasitism, saprobism,
and the development of mutualistic relationships such as mycorrhiza and lichenization.
Recent studies suggest that the ancestral ecological state of the Ascomycota was saprobism,
and that independent lichenization events have occurred multiple times.
It is presumed that the fungi colonized the land during the Cambrian, long before land plants.
Fossilized hyphae and spores recovered
from the Ordovician of Wisconsin resemble modern-day Glomerales, and existed at a time
when the land flora likely consisted of only non-vascular bryophyte-like plants. Prototaxites,
which was probably a fungus or lichen, would have been the tallest organism of the late Silurian.
Fungal fossils do not become common and uncontroversial until the early Devonian,
when they occur abundantly in the Rhynie chert, mostly as Zygomycota and Chytridiomycota.
At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,
and all modern classes of fungi were present by the Late Carboniferous.
Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back
to 635–551 Ma. Lichens formed a component of the early terrestrial ecosystems,
and the estimated age of the oldest terrestrial lichen fossil is 400 Ma; this date corresponds
to the age of the oldest known sporocarp fossil,
a Paleopyrenomycites species found in the Rhynie Chert. The oldest fossil
with microscopic features resembling modern-day basidiomycetes is Palaeoancistrus,
found permineralized with a fern from the Pennsylvanian.
Rare in the fossil record are the Homobasidiomycetes.
Two amber-preserved specimens provide evidence that the earliest known mushroom-forming fungi
appeared during the late Cretaceous, 90 Ma.
Some time after the Permian–Triassic extinction event, a fungal spike formed,
suggesting that fungi were the dominant life form at this time,
representing nearly 100% of the available fossil record for this period. However,
the relative proportion of fungal spores relative to spores formed by algal species is difficult
to assess, the spike did not appear worldwide,
and in many places it did not fall on the Permian–Triassic boundary.
 Taxonomy 
Although commonly included in botany curricula and textbooks, fungi are more closely related
to animals than to plants and are placed
with the animals in the monophyletic group of opisthokonts.
Analyses using molecular phylogenetics support a monophyletic origin of the Fungi.
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.
There is no unique generally accepted system at the higher taxonomic levels
and there are frequent name changes at every level, from species upwards.
Efforts among researchers are now underway to establish and encourage usage of a unified
and more consistent nomenclature.
Fungal species can also have multiple scientific names depending on their life cycle
and mode of reproduction. Web sites such as Index Fungorum
and ITIS list current names of fungal species.
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.
It recognizes seven phyla, two of which—the Ascomycota
and the Basidiomycota—are contained within a branch representing subkingdom Dikarya,
the most species rich and familiar group, including all the mushrooms, most food-spoilage molds,
most plant pathogenic fungi, and the beer, wine, and bread yeasts.
The accompanying cladogram depicts the major fungal taxa and their relationship to opisthokont
and unikont organisms, based on the work of Philippe Silar and
"The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic
and Applied Research". The lengths of the branches are not proportional to evolutionary distances.
 Taxonomic groups 
The major phyla of fungi have been classified mainly on the basis of characteristics of their
sexual reproductive structures. Currently, seven phyla are proposed: Microsporidia,
Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Glomeromycota, Ascomycota,
and Basidiomycota.  [^]  Phylogenetic analysis has demonstrated that the Microsporidia,
unicellular parasites of animals and protists, are fairly recent
and highly derived endobiotic fungi.
One 2006 study concludes that the Microsporidia are a sister group to the true fungi; that is,
they are each other's closest evolutionary relative. Hibbett
and colleagues suggest that this analysis does not clash with their classification of the Fungi,
and although the Microsporidia are elevated to phylum status,
it is acknowledged that further analysis is required
to clarify evolutionary relationships within this group.
The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide.
Chytrids and their close relatives Neocallimastigomycota and Blastocladiomycota are the only fungi
with active motility,
producing zoospores that are capable of active movement through aqueous phases
with a single flagellum, leading early taxonomists to classify them as protists.
Molecular phylogenies, inferred from rRNA sequences in ribosomes,
suggest that the Chytrids are a basal group divergent from the other fungal phyla,
consisting of four major clades with suggestive evidence for paraphyly or possibly polyphyly.
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.
The blastocladiomycetes are saprotrophs, feeding on decomposing organic matter,
and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids,
most of which exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis.
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 in other terrestrial
and aquatic environments enriched in cellulose. They lack mitochondria,
but contain hydrogenosomes of mitochondrial origin. As in the related chrytrids,
neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.
Members of the Glomeromycota form arbuscular mycorrhizae,
a form of mutualist symbiosis wherein fungal hyphae invade plant root cells
and both species benefit from the resulting increased supply of nutrients.
All known Glomeromycota species reproduce asexually.
The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating
to 400 million years ago. Formerly part of the Zygomycota, the Glomeromycota were elevated
to phylum status in 2001 and now replace the older phylum Zygomycota.
Fungi that were placed in the Zygomycota are now being reassigned to the Glomeromycota,
or the subphyla incertae sedis Mucoromycotina, Kickxellomycotina, the Zoopagomycotina
and the Entomophthoromycotina.
Some well-known examples of fungi formerly in the Zygomycota include black bread mold,
and Pilobolus species, capable of ejecting spores several meters through the air.
Medically relevant genera include Mucor, Rhizomucor, and Rhizopus.  [^]  The Ascomycota,
commonly known as sac fungi or ascomycetes,
constitute the largest taxonomic group within the Eumycota.
These fungi form meiotic spores called ascospores,
which are enclosed in a special sac-like structure called an ascus. This phylum includes morels,
a few mushrooms and truffles, unicellular yeasts,
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,
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. 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.
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