The fungi (singular fungus) are a kingdom of eukaryotic organisms. They are heterotrophic and digest their food externally, absorbing nutrient molecules into their cells. Yeasts, molds, and mushrooms are examples of fungi. The branch of biology involving the study of fungi is known as mycology.
Fungi often have important symbiotic relationships with other organisms. Mycorrhizal symbiosis between plants and fungi is particularly important; over 90% of all plant species engage in some kind of mycorrhizal relationship with fungi and are dependent upon this relationship for survival. Fungi are also used extensively by humans: yeasts are responsible for fermentation of beer and bread, and mushroom farming and gathering is a large industry in many countries.
Phylogeny and classification of fungi
Fungi were originally classified as plants, however they have since been separated as they are heterotrophs. This means they do not fix their own carbon through photosynthesis, but use carbon fixed by other organisms for metabolism. Fungi are now thought to be more closely related to animals than to plants, and are placed with animals in the monophyletic group of opisthokonts. For much of the Paleozoic Era, the fungi appear to have been aquatic. The first land fungi probably appeared in the Silurian, right after the first land plants appeared, even though their fossils are fragmentary. Fungi absorb their food while animals ingest it; also unlike animals, the cells of fungi have cell walls. For these reasons, these organisms are placed in their own kingdom, Fungi, or Eumycota.
The Fungi are a monophyletic group, meaning all varieties of fungi come from a common ancestor. The monophyly of the fungi has been confirmed through repeated tests of molecular phylogenetics; shared ancestral traits include chitinous cell walls and heterotrophy by absorption, along with other shared characteristics.
The taxonomy of the Fungi is in a state of rapid flux at present, especially due to recent papers based on DNA comparisons, which often overturn the assumptions of the older systems of classification. There is no unique generally accepted system at the higher taxonomic levels and there are constant name changes at every level, from species upwards. Web sites such as Index Fungorum, ITIS and Wikispecies define preferred up-to-date names (with cross-references to older synonyms), but do not always agree with each other or with names in Wikipedia in its various language variants.
Types of fungi
- The Chytridiomycota are commonly known as chytrids. These fungi produce zoospores that are capable of moving on their own through liquid menstrua by simple flagella.
- The Zygomycota are known as zygomycetes 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 shoots specialized structures through the air for several meters. Medically relevant genera include Mucor, Rhizomucor, and Rhizopus. Molecular phylogenetic investigation has shown the zygomycota to be a polyphyletic group.
- Members of the Glomeromycota are also known as the arbuscular mycorrhizal fungi. Only one species has been observed forming zygospores; all other species only reproduce asexually. This is an ancient association, with evidence dating to 350 million years ago.
- The Ascomycota, commonly known as sac fungi or ascomycetes, form meiotic spores called ascospores, which are enclosed in a special sac-like structure called an ascus. This division includes morels, some mushrooms and truffles, as well as single-celled yeasts and many species that have only been observed undergoing asexual reproduction. 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.
Although the water moulds and slime moulds 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 water moulds and slime moulds do not have cell walls made of chitin. In the 5-kingdom system, they are currently placed in the kingdom Protista. Water moulds are descended from algae, and are placed within the phylum Oomycota, within the Kingdom Protista.
Fungi may reproduce sexually or asexually. In asexual reproduction, the offspring are genetically identical to the “parent” organism (they are clones). During sexual reproduction, a mixing of genetic material occurs so that the offspring exhibit traits of both parents. Many species can use both strategies at different times, while others are apparently strictly sexual or strictly asexual. Sexual reproduction has not been observed in some fungi of the Glomeromycota and Ascomycota. These are commonly referred to as Fungi imperfecti or Deuteromycota.
Yeasts and other unicellular fungi can reproduce simply by budding, or “pinching off” a new cell. Many multicellular species produce a variety of different asexual spores that are easily dispersed and resistant to harsh environmental conditions. When the conditions are right, these spores will germinate and colonize new habitats.
Sexual reproduction in fungi is somewhat different from that of animals or plants, and each fungal division reproduces using different strategies. Fungi that are known to reproduce sexually all have a haploid stage and a diploid stage in their life cycles. Ascomycetes and basidiomycetes also go through a dikaryotic stage, in which the nuclei inherited by the two parents do not fuse right away, but remain separate in the hyphal cells (see heterokaryosis).
In zygomycetes, the haploid hyphae of two compatible individuals fuse, forming a zygote, which becomes a resistant zygospore. When this zygospore germinates, it quickly undergoes meiosis, generating new haploid hyphae and asexual sporangiospores. These sporangiospores may then be distributed and germinate into new genetically-identical individuals, each producing their own haploid hyphae. When the hyphae of two compatible individuals come into contact with one another, they will fuse and generate new zygospores, thus completing the cycle.
In ascomycetes, when compatible haploid hyphae fuse with one another, their nuclei do not immediately fuse. The dikaryotic hyphae form structures called 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 to form new haploid mycelium. Asexual conidia may be produced by the haploid mycelium. Many ascomycetes appear to have lost the ability to reproduce sexually and reproduce only via conidia.
Sexual reproduction in basidiomycetes is similar to that of ascomycetes. Sexually compatible haploid hyphae fuse to produce a dikaryotic mycelium. This leads to the production of a basidiocarp. The most commonly-known basidiocarps are mushrooms, but they may also take many other forms. Club-like structures known as basidia generate haploid basidiospores following karyogamy and meiosis. These basidiospores then germinate to produce new haploid mycelia.
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.
Many fungi are important as partners in symbiotic relationships with other organisms, as mutualists, parasites, or commensalists, as well as in symbiotic relationships that do not fall neatly into any of these categories. One of the most important of these relationships are various types of mycorrhiza, which is a kind of mutualistic relationship between fungi and plants, in which the plant's roots are closely associated with fungal hyphae and other structures. The plant donates to the fungus sugars and other carbohydrates that it manufactures from photosynthesis, while the fungus donates water and mineral nutrients that the hyphal network is able to find much more efficiently than the plant roots alone can, particularly phosphorus. The fungi also protect against diseases and pathogens and provide other benefits to the plant. Recently, plants have been found to use mycorrhizas to deliver carbohydrates and other nutrients to other plants in the same community and in some cases can make plant species that would normally exclude each other able to coexist in the same plant community. Such mycorrhizal communities are called "common mycorrhizal networks". Over 90% of the plant species on Earth are dependent on mycorrhizae of one type or another in order to survive, and it is hypothesized that the presence of terrestrial fungi may have been necessary in order for the first plants to colonize land.
Lichens are formed by a symbiotic relationship between algae or cyanobacteria (referred to in lichens as "photobionts") and fungi (mostly ascomycetes of various kinds and a few basidiomycetes), in which individual photobiont cells are embedded in a complex of fungal tissue. 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.
Certain insects also engage in mutualistic relationships with various types of fungi. Several groups of ants cultivate various fungi in the Agaricales as their primary food source, while ambrosia beetles cultivate various kinds of fungi in the bark of trees that they infest. 
Some fungi are parasites on plants, animals (including humans), and even other fungi. Pathogenic fungi are responsible for numerous diseases, such as athlete’s foot and ringworm in humans and Dutch elm disease in plants. Some fungi are predators of nematodes, which they capture using an array of devices such as constricting rings or adhesive nets .
Human uses of fungi
Fungi have a long history of use by humans. Many types of mushrooms and other fungi are eaten, including button mushrooms, shiitake mushrooms, and oyster mushrooms. Of course, many species of mushrooms are poisonous and are responsible for numerous cases of sickness and death every year. A type of single-celled fungus called yeast is used in baking bread and fermenting alcoholic beverages, while mycelial fungus is used to make Shoyu (soy sauce) and tempeh. Fungi are also used to produce industrial chemicals like lactic acid, antibiotics and even to make stonewashed jeans. Some types of fungi are ingested for their psychedelic properties, both recreationally and religiously (see main article, Psychedelic mushroom).
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. Button mushrooms (Agaricus bisporus) are the most commonly eaten species, used in salads, soups, and many other dishes. Portobello mushrooms are the same species, but are allowed to grow to a much larger size. 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 command a high price on the market. They are often used in gourmet dishes.
It is also a common practice to permit the growth of specific species of mold in certain types of cheeses that give them their unique flavor. This mold is non-toxic and is safe for human consumption. This accounts for the blue colour in cheeses such as Roquefort or Stilton.
Hundreds of mushroom species are toxic to humans, causing anything from upset stomachs to hallucinations to death. Some of the most deadly belong to the genus Amanita, including A. virosa (the "destroying angel") and A. phalloides (the "death cap"). Stomach cramps, vomiting, and diarrhea usually occur within 6-24 hours after ingestion of these mushrooms, followed by a brief period of remission (usually 1-2 days). Patients often fail to present themselves for treatment at this time, assuming that they have recovered. However, within 2-4 weeks liver and kidney failure leads to death if untreated. There is no antidote for the toxins in these mushrooms, but kidney dialysis and administration of corticosteroids may help. In severe cases, a liver transplant may be necessary (Kaminstein 2002). 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 leave it alone.
Fly agaric mushrooms (A. muscaria) are also responsible for a large number of poisonings, but these cases rarely result in death. The most common symptoms are nausea and vomiting, drowsiness, and hallucinations. In fact, this species is used ritually and recreationally for its hallucinogenic properties. However, if it is taken in over a long period of time (regularly over more than six months), this species might cause a temporary loss of sight, which can last from several minutes to an hour.
Fungi in the biological control of pests
Many fungi compete with other organisms, or directly infect them. Some of these fungi are considered beneficial because they can restrict, and sometimes eliminate, the populations of noxious organisms like pest insects, mites, weeds, nematodes and other fungi, such as those that kill plants. There is much interest on the manipulation of these beneficial fungi for the biological control of pests. Some of these fungi can be used as biopesticides, like the ones that kill insects (entomopathogenic fungi). Specific examples of fungi that have been developed as bioinsecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella, Paecilomyces fumosoroseus, and Verticillium lecanii (=Lecanicillium lecanii).
- Volk, Tom. Tom Volk's Fungi FAQ. Retrieved on 2006-09-21., University of Wisconsin, Department of Botany, "Even more important are the mushrooms that are associated with trees as mycorrhizae. Without this mutualistic association most trees would not survive. Killing these fungi would effectively kill your trees."
- Wong, George. Symbiosis: Mycorrhizae and Lichens. Retrieved on 2006-09-21., University of Hawaii at Manoa, Botany Department, "[Mycorrhizae occur] in practically all plants with the exception of the Brassicaceae; The Crucifer Family; Chenopodiaceae, The Goosefoot Family; Cyperaceae; The Sedge Family and in aquatic plants. All other families form mycorrhizae. It is believed that for many plants that usually form mycorrhizae, they would be unable to survive in their natural habitat without this symbiotic relationship."
- See Palaeos: Fungi for an introduction to fungal taxonomy, including recent controversies.
- Deacon JW. (2005). Fungal Biology (4th ed). Malden, MA: Blackwell Publishers. ISBN 1-4051-3066-0.
- Kaminstein D. (2002). Mushroom poisoning.
- The WWW Virtual Library: Mycology
- MykoWeb: Mycological Links
- Tom Volk's Fungi
- Illinois Mycological Association Mycological Glossary
- "Introduction to the Fungi", University of California Museum of Paleontology.
- Fungal Biology, University of Sydney, School of Biological Sciences, June, 2004. – Online textbook
- The Fifth Kingdom – Online textbook
- Australian National Botanic Gardens Fungi Web Site – Online textbook
- Pacific Northwest Fungi, Online Journal
- North American Mycological Association
- Mycological Society of America
- British Mycological Society
- Sydney Fungal Studies Group
- fungi as mycobionts in lichens
- CABI Bioscience Databases - Includes Index Fungorum genus and species names and top-down hierarchy
- Mushroom Observer - A site for recording observations of mushrooms and getting help identifying unknown collections