The Fungus Kingdom

A fungus (plural fungi) is a eukaryotic organism that digests its food externally and absorbs the nutrient molecules into its cells. Along with bacteria, fungi are the primary decomposers of dead organic matter in most terrestrial ecosystems. Many fungi have important symbiotic relationships with many 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.

The branch of biology involving the study of fungi is known as mycology.

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 be 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, and their cells have cell walls. For these reasons, these organisms are placed in their own kingdom, Fungi.

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 major divisions (phyla) of fungi are mainly classified based on their sexual reproductive structures. Currently, five divisions are recognized:

Although the water molds and slime molds have traditionally been placed in kingdom Fungi and are still studied by mycologists, they are not true fungi. Unlike true fungi, the water molds and slime molds do not have cell walls made of chitin. In the 5-kingdom system, they are currently placed in kingdom Protista. Water molds are descended from algae, and are placed within the phylum Oomycota, within the Kingdom Protista.

Structure

Fungi may be single-celled or multicellular. Multicellular fungi are composed of networks of long hollow tubes called hyphae. The hyphae often aggregate in a dense network known as a mycelium. The mycelium grows through the medium on which the fungus feeds. Because fungi are embedded in the medium in which they grow, they are often not visible to the naked eye.

Although fungi lack true organs, the mycelia of ascomycetes and basidiomycetes may become organized into more complex reproductive structures called fruiting bodies, or sporocarps, when conditions are right. "Mushroom" is the common name given to the above-ground fruiting bodies of many fungal species. Although these above-ground structures are the most conspicuous to humans, they make up only a small portion of the entire fungal body. Some fungi form rhizoids, which are underground root-like structures that provide support and transport nutrients from the soil to the rest of the mycelium.

A fungus of the species Armillaria ostoyae may be the largest organism on the planet. It was discovered in the Malheur National Forest in Oregon, and its underground mycelial network covers an area of 8.9 km² (2200 acres)^[4]. Whether or not this is an actual individual organism is disputed: some tests have indicated that they have the same genetic makeup ^[5], but this does not exclude its being a clonal colony of numerous smaller individuals.

Reproduction

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.

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.

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 critically 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 enoki mushrooms (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 ).