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    Fungus Experiments

    Fungus Background Information

    Definition

    A fungus (plural fungi) is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms.

    Basics

    A Fungus (plural: Fungi) is a kind of living organism: yeasts, moulds and mushrooms are types of fungi. The Fungi are a separate Kingdom of living things, different from animals and plants.

    Fungi have cells with nuclei; their cell walls contain chitin. Their basic mode of life is saprophytic: a fungus breaks down the dead matter around it and uses it as food.

    Reproduction: Fungi reproduce both sexually and asexually. Some fungi grow mushrooms: these are fruiting bodies. Under the cap there are gills; the gills bear spores that will disperse, and may develop into new fungi.

    Fungal states: Two fungal states exist: the unicellular or "yeast" form and the mycelial form. The yeast form is single-celled and reproduction occurs by simple budding or binary fission. The mycelial form is the vegetative growth of filaments, which may develop fruiting bodies (for instance, mushrooms) at times.

    Uses

    • Edible fungi are widely used as human food. Certain types of cheese need a fungal species to be added. The fungi give a unique flavor and texture to the cheese.
    • Some fungi produce psychotropic (mind-altering) substances. Several species, most notably Psilocybin mushrooms (colloquially known as magic mushrooms), are taken for their psychedelic properties.
    • In modern times, some fungi (for example, Penicillin) have been used as a source of antibiotics. The antibiotics are produced by many fungi as a natural defence against bacteria.

    Pathogens: is highly poisonousSome fungi cause crop diseases; others cause serious disease in humans. Some are highly poisonous: never eat a mushroom picked in the wild unless you know what you are doing.

    Symbiosis means living together. Some fungi can come together with an alga to form a lichen. In this partnership the algal cells live inside the fungus tissue. The end result is a new mat-like life-form which clings to rock and other surfaces. About 20% of all fungi are lichenized. Another important kind of symbiosis is mycorrhiza. This is when a fungus lives inside plant roots; many trees have mycorrhizal roots. Both sides benefit in this arrangement.

    Topics of Interest

    A fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. The Fungi are classified as a kingdom that is separate from plants, animals and bacteria. One major difference is that fungal cells have cell walls that contain chitin, unlike the cell walls of plants, which contain cellulose. These and other differences show that the fungi form a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (a monophyletic group). This fungal group is distinct from the structurally similar slime molds (myxomycetes) and water molds (oomycetes). The discipline of biology devoted to the study of fungi is known as mycology, which is often regarded as a branch of botany, even though genetic studies have shown that fungi are 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, on dead matter, and as symbionts of plants, animals, or other fungi. They may become noticeable when fruiting, either as mushrooms or molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange. They have long been used as a direct source of food, such as mushrooms and truffles, as a leavening agent for bread, and in 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 agents to control weeds and 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 (e.g. rice blast disease) 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 single-celled aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at around 1.5 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 (e.g., characteristics such as spore color or microscopic features) 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 of Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla.

    The English word fungus is directly adopted from the Latin fungus (mushroom), used in the writings of Horace and Pliny. This in turn is derived from the Greek word sphongos ("sponge"), 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 ("sponge"), Schimmel ("mold"), and the French champignon and the Spanish champińon (which both mean "mushroom"). The use of the word mycology, which is derived from the Greek mykes (mushroom) and logos (discourse), 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.

    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 fruiting bodies, which sometimes bear resemblance to 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.

    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. 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.

    Microscopic structures: A hypha of Hyaloperonospora parasitica (downy mildew) growing within the leaf tissue of Arabidopsis thaliana. The long structure is the hypha, and the little spheres are haustoria, which extract nutrients from the plant cells.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 (apices); new hyphae are typically formed by emergence of new tips along existing hyphae by a process called branching, or occasionally growing hyphal tips bifurcate (fork) giving rise to two parallel-growing hyphae. The combination of apical growth and branching/forking leads 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 (internal cell walls, called septa, that are formed at right angles to the cell wall giving the hypha its shape), 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 the fungi of the phylum Basidiomycota. Coenocytic hyphae are essentially multinucleate supercells.

    Macroscopic structures: Armillaria ostoyaeFungal mycelia can become visible to the naked eye, for example, on various surfaces and substrates, such as damp walls and on spoilt food, where they are commonly called mold. Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies. These colonies can exhibit growth shapes and colors (due to spores or pigmentation) 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 ostoyae, which extends over an area of more than 900 ha, with an estimated age of nearly 9,000 years.

    Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this kingdom of organisms. It is estimated that a third of all fungi reproduce by different modes 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.

    Asexual reproduction via vegetative spores (conidia) or through mycelial fragmentation is common; it maintains clonal populations adapted to a specific niche, and allows more rapid dispersal than sexual reproduction. The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species which lack an observable sexual cycle.

    Sexual reproduction with meiosis exists in all fungal phyla (with the exception of the Glomeromycota). It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and can be used to discriminate species by morphological differences in sexual structures and reproductive strategies. Mating experiments between fungal isolates may identify species on the basis of 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. Some species may 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.

    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.

    Evolution: Fungi diverged from other life around 1,500 million years ago, with the glomaleans branching from the "higher fungi" at ~570 million years ago, according to DNA analysis. Fungi probably colonised the land during the Cambrian, over 500 million years ago, but fossils only become uncontroversial and common during the Devonian, 400 million years ago.

    A rich diversity of fungi is known from the lower Devonian Rhynie chert, an earlier record is absent. Since fungi don't biomineralise, they do not readily enter the fossil record; only three claims of early fungi. One from the Ordovician has been dismissed on the grounds that it lacks any distinctly fungal features, and is held by many to be contamination; the position of a "probable" Proterozoic fungus is still not established, and it may represent a stem group fungus. There is also a case for a fungal affinity for the enigmatic microfossil Ornatifilum. Since the fungi form a sister group to the animals, the two lineages must have diverged before the first animal lineages, which are known from fossils as early as the Ediacaran.

    Taxonomy: 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. 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.

    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 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.

    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 and in many food webs. As decomposers, they play an essential 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.

    Symbiosis: Many fungi have important symbiotic relationships with organisms from most if not all Kingdoms. 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.

    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.

    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. Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession, and are the dominating life forms in extreme environments, including polar, alpine, and semiarid desert regions. They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves. As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis, 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.

    Many insects also engage in mutualistic relationships with 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. Similarly, females of several wood wasp species (genus Sirex) inject their eggs together with spores of the wood-rotting fungus Amylostereum areolatum into the sapwood of pine trees; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae. Termites on the African savannah are also known to cultivate fungi, and yeasts of the genera Candida and Lachancea inhabit the gut of a wide range of insects, including neuropterans, beetles, and cockroaches; it is not known whether these fungi benefit their hosts.

    The human use of fungi for food preparation or preservation and other purposes is extensive and has a long history. Mushroom farming and mushroom gathering are large industries in many countries. The study of the historical uses and sociological impact of fungi is known as ethnomycology. Because of the capacity of this group to produce an enormous range of natural products with antimicrobial or other biological activities, many species have long been used or are being developed for industrial production of antibiotics, vitamins, and anti-cancer and cholesterol-lowering drugs. More recently, methods have been developed for genetic engineering of fungi, enabling metabolic engineering of fungal species. For example, genetic modification of yeast species—which are easy to grow at fast rates in large fermentation vessels—has opened up ways of pharmaceutical production that are potentially more efficient than production by the original source organisms.

    Many mushroom species are poisonous to humans, with toxicities ranging from slight digestive problems or allergic reactions as well as hallucinations to severe organ failures and death. Genera with mushrooms containing deadly toxins include Conocybe, Galerina, Lepiota, 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. The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw. Tricholoma equestre was considered edible until being implicated in serious poisonings causing rhabdomyolysis. Fly agaric mushrooms (Amanita muscaria) also cause occasional non-fatal poisonings, mostly as a result of ingestion for use as a recreational drug for its hallucinogenic properties. Historically, fly agaric was used by different peoples in Europe and Asia and its present usage for religious or shamanic purposes is reported from some ethnic groups such as the Koryak people of north-eastern Siberia.

    As it is difficult to accurately identify a safe mushroom without proper training and knowledge, it is often advised to assume that a wild mushroom is poisonous and not to consume it.

    Pest control: Grasshoppers killed by Beauveria bassianaIn agriculture, fungi may be useful if they actively compete for nutrients and space with pathogenic microorganisms such as bacteria or other fungi via the competitive exclusion principle, or if they are parasites of these pathogens. For example, certain species may be used to eliminate or suppress the growth of harmful plant pathogens, such as insects, mites, weeds, nematodes and other fungi that cause diseases of important crop plants. This has generated strong interest in practical applications that use these fungi in the biological control of these agricultural pests. Entomopathogenic fungi can be used as biopesticides, as they actively kill insects. Examples that have been used as biological insecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella spp, Paecilomyces spp, and Verticillium lecanii. 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. 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.

    Mycoremediation is a form of bioremediation, the process of using fungi to return an environment (usually soil) contaminated by pollutants to a less contaminated state. The term mycoremediation was coined by Paul Stamets and refers specifically to the use of fungal mycelia in bioremediation.

    Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License and Creative Commons Attribution-ShareAlike License.)

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