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A 90-barrel fermentation tank holds 60 barrels of Quayside Kölsch.
Lorton (Fairfax County), Virginia.
9 October 2015.
▶ More photos: here.
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▶ Kölsch is
"a top-warm-fermented [ale], cold-aged [like a lager], with a very pale golden color, although a little darker than a Pilsner and an alcohol content of 4.4 to 4.9% by volume. The beer has an aromatic bitterness and noticeable hop character (16-34 IBUs), is well fermented, and is lagered cold for 14 to 60 days. It combines the pale color of a fine Pilsner with the fruitiness of a fine ale."
— Encyclopedia of Beer (1995).
Christine Rhodes, et al.
▶ "Quayside" is pronounced "keyside." The term refers to the land bordering a quay (again, pronounced, "key"), a place for boats to stop for loading and unloading. Fair Winds Brewing's owner, Casey Jones, served in the U.S. Coast Guard. That influence shows.
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▶ Photo by Yours For Good Fermentables.com.
▶ For a larger image, type 'L' (without the quotation marks).
— Like on Facebook: YoursForGoodFermentables.
— Follow on Instagram: @tcizauskas.
▶ Camera: Olympus Pen E-PL1.
— Lens: Olympus M.14-42mm F3.5-5.6 II L
— Focal length: 29 mm
— Aperture: ƒ/4.7
— Shutter speed: 1/60
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▶ Commercial use requires explicit permission, as per Creative Commons.
My new Morebeer domed conical lid after adding a 1.5" ferrule for my thermowell. A 1.5" cap was drilled and the thermowell welded into place.
Transferred cider to 5 gallon carboys yesterday. It's great to have the major effort of pressing behind us, but bottling, which is no picnic, still remains. We won't be bottling until the cider has fermented to dryness, around March or so.
We picked up a salted fish from Thailand and it was pretty good! It turned out to be 梅香咸鱼 fermented salted fish, stronger in flavour, but quite prized for it's pungency! :)
One or two cubic centimetres of this stuff would be perfect with a bowl of rice :)
Not bad steamed with tofu either, whose plain flavour was a nice compliment!
Making room and a fairly uniform surface in the mash tun for the manifold. Note the power drill in upper left.
This particular pumpkin fermenter holds approximately three gallons of wort. Once the wort is in the fermenter, beer yeast -- specifically, Danstar's Nottingham ale yeast -- is pitched and the wort is aerated to increase the oxygen available to the yeast.
A fungus (pl.: fungi or funguses) 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 one of the traditional eukaryotic kingdoms, along with Animalia, Plantae and either Protista or Protozoa and Chromista.
A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), 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 (true fungi or Eumycetes), that share a common ancestor (i.e. they form a monophyletic group), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek μύκης mykes, mushroom). In the past mycology was regarded as a branch of botany, although it is now known that 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 (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 unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of the fungus kingdom, which has been estimated at 2.2 million to 3.8 million species. Of these, only about 148,000 have been described, with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. Ever since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christiaan 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 first decade of the 21st century have helped reshape the classification within the fungi kingdom, which is divided into one subkingdom, seven phyla, and ten subphyla.
Etymology
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 (σφόγγος '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') and Schimmel ('mold').
The word mycology is derived from the Greek mykes (μύκης 'mushroom') and logos (λόγος 'discourse'). It denotes the scientific study of fungi. The Latin adjectival form of "mycology" (mycologicæ) appeared as early as 1796 in a book on the subject by Christiaan Hendrik Persoon. The word appeared in English as early as 1824 in a book by Robert Kaye Greville. In 1836 the English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward Smith, Vol. 5. also refers to mycology as the study of fungi.
A group of all the fungi present in a particular region is known as mycobiota (plural noun, no singular). The term mycota is often used for this purpose, but many authors use it as a synonym of Fungi. The word funga has been proposed as a less ambiguous term morphologically similar to fauna and flora. The Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN) in August 2021 asked that the phrase fauna and flora be replaced by fauna, flora, and funga.
Characteristics
Fungal hyphae cells
Hyphal wall
Septum
Mitochondrion
Vacuole
Ergosterol crystal
Ribosome
Nucleus
Endoplasmic reticulum
Lipid body
Plasma membrane
Spitzenkörper
Golgi apparatus
Fungal cell cycle showing Dikaryons typical of Higher Fungi
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. Although inaccurate, the common misconception that fungi are plants persists among the general public due to their historical classification, as well as several similarities. 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 (around the start of the Neoproterozoic Era). 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:
With other eukaryotes: Fungal cells contain membrane-bound nuclei with chromosomes that contain DNA with noncoding regions called introns and coding regions called exons. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes, and ribosomes of the 80S type. They have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols (e.g., mannitol), disaccharides, (e.g., trehalose), and polysaccharides (e.g., glycogen, which is also found in animals).
With animals: Fungi lack chloroplasts and are heterotrophic organisms and so require preformed organic compounds as energy sources.
With plants: Fungi have a cell wall and vacuoles. They reproduce by both sexual and asexual means, and like basal plant groups (such as ferns and mosses) produce spores. Similar to mosses and algae, fungi typically have haploid nuclei.
With euglenoids and bacteria: Higher fungi, euglenoids, and some bacteria produce the amino acid L-lysine in specific biosynthesis steps, called the α-aminoadipate pathway.
The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures called hyphae, which may contain multiple nuclei and extend by growing at their tips. Each tip contains a set of aggregated vesicles—cellular structures consisting of proteins, lipids, and other organic molecules—called the Spitzenkörper. Both fungi and oomycetes grow as filamentous hyphal cells. In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells. There are also single-celled fungi (yeasts) that do not form hyphae, and some fungi have both hyphal and yeast forms.
In common with some plant and animal species, more than one hundred fungal species display bioluminescence.
Unique features:
Some species grow as unicellular yeasts that reproduce by budding or fission. Dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions.
The fungal cell wall is made of a chitin-glucan complex; while glucans are also found in plants and chitin in the exoskeleton of arthropods, fungi are the only organisms that combine these two structural molecules in their cell wall. Unlike those of plants and oomycetes, fungal cell walls do not contain cellulose.
A whitish fan or funnel-shaped mushroom growing at the base of a tree.
Omphalotus nidiformis, a bioluminescent mushroom
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 that 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 fungi Batrachochytrium dendrobatidis and B. salamandrivorans, parasites that have been responsible for a worldwide decline in amphibian populations. These organisms spend part of their life cycle as a motile zoospore, enabling them to propel itself through water and enter their amphibian host. Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.
As of 2020, around 148,000 species of fungi have been described by taxonomists, but the global biodiversity of the fungus kingdom is not fully understood. A 2017 estimate suggests there may be between 2.2 and 3.8 million species The number of new fungi species discovered yearly has increased from 1,000 to 1,500 per year about 10 years ago, to about 2000 with a peak of more than 2,500 species in 2016. In the year 2019, 1882 new species of fungi were described, and it was estimated that more than 90% of fungi remain unknown The following year, 2905 new species were described—the highest annual record of new fungus names. 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.
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 (Fomes fomentarius), or for medicinal purposes (Piptoporus betulinus). 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 became a systematic science 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 (1753), the Dutch Christiaan Hendrik Persoon (1761–1836) established the first classification of mushrooms with such skill as to be considered a founder of modern mycology. Later, Elias Magnus Fries (1794–1878) further elaborated the classification of fungi, using spore color and 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. In the 20th and 21st centuries, advances in biochemistry, genetics, molecular biology, biotechnology, DNA sequencing and phylogenetic analysis has provided new insights into fungal relationships and biodiversity, and has challenged traditional morphology-based groupings in fungal taxonomy.
Morphology
Microscopic structures
Monochrome micrograph showing Penicillium hyphae as long, transparent, tube-like structures a few micrometres across. Conidiophores branch out laterally from the hyphae, terminating in bundles of phialides on which spherical condidiophores are arranged like beads on a string. Septa are faintly visible as dark lines crossing the hyphae.
An environmental isolate of Penicillium
Hypha
Conidiophore
Phialide
Conidia
Septa
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 fork, giving rise to two parallel-growing hyphae. Hyphae also sometimes fuse when they come into contact, a process called hyphal fusion (or anastomosis). 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 (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 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,[63] 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 (e.g., β-1,3-glucan) 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 (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 solidipes, which extends over an area of more than 900 ha (3.5 square miles), 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 (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well known as mushrooms.
Growth and physiology
Time-lapse photography sequence of a peach becoming progressively discolored and disfigured
Mold growth covering a decaying peach. The frames were taken approximately 12 hours apart over a period of six days.
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.[71] The pressure generated by the appressorium, directed against the plant epidermis, can exceed 8 megapascals (1,200 psi).[71] 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 (extending in one direction) by elongation at the tip (apex) of the hypha. Other forms of fungal growth include intercalary extension (longitudinal expansion of hyphal compartments that are below the apex) 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 (see above) and biofilms for substrate colonization and intercellular communication.
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
Two thickly stemmed brownish mushrooms with scales on the upper surface, growing out of a tree trunk
Polyporus squamosus
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 (sexual reproduction) and the anamorph (asexual reproduction). 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
Asexual reproduction occurs via vegetative spores (conidia) or through mycelial fragmentation. Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each component grows into a separate mycelium. Mycelial fragmentation and vegetative spores maintain clonal populations adapted to a specific niche, and allow more rapid dispersal than sexual reproduction. The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species that lack an observable sexual cycle. Deuteromycota (alternatively known as Deuteromycetes, conidial fungi, or mitosporic fungi) is not an accepted taxonomic clade and is now taken to mean simply fungi that lack a known sexual stage.
Sexual reproduction
See also: Mating in fungi and Sexual selection in fungi
Sexual reproduction with meiosis has been directly observed in all fungal phyla except Glomeromycota (genetic analysis suggests meiosis in Glomeromycota as well). 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. Fungi employ two mating systems: heterothallic species allow mating only between individuals of the opposite mating type, whereas homothallic species can mate, and sexually reproduce, with any other individual or itself.
Most fungi have both a haploid and a diploid stage in their life cycles. In sexually reproducing fungi, compatible individuals may combine by fusing their hyphae together into an interconnected network; this process, anastomosis, is required for the initiation of the sexual cycle. Many ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells (see heterokaryosis).
In ascomycetes, dikaryotic hyphae of the hymenium (the spore-bearing tissue layer) form a characteristic hook (crozier) at the hyphal septum. During cell division, the formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. Asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. After dispersal, the ascospores may germinate and 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, often also present in the vegetatively growing mycelium. A specialized anatomical structure, called a clamp connection, is formed at each hyphal septum. As with the structurally similar hook in the ascomycetes, the clamp connection in the basidiomycetes is required for controlled transfer of nuclei during cell division, to maintain the dikaryotic stage with two genetically different nuclei in each hyphal compartment. A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis. The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).
In fungi formerly classified as Zygomycota, haploid hyphae of two individuals fuse, forming a gametangium, a specialized cell structure that becomes a fertile gamete-producing cell. The gametangium develops into a zygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which may then form asexual sporangiospores. These sporangiospores allow the fungus to rapidly disperse and germinate into new genetically identical haploid fungal mycelia.
Spore dispersal
The spores of most of the researched species of fungi are transported by wind. Such species often produce dry or hydrophobic spores that do not absorb water and are readily scattered by raindrops, for example. In other species, 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 (such as hydrophobins), 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 (Buller's drop), 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 hydnoid fungi (tooth fungi) produce spores on pendant, tooth-like or spine-like projections. 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.
Homothallism
In homothallic sexual reproduction, two haploid nuclei derived from the same individual fuse to form a zygote that can then undergo meiosis. Homothallic fungi include species with an Aspergillus-like asexual stage (anamorphs) occurring in numerous different genera, several species of the ascomycete genus Cochliobolus, and the ascomycete Pneumocystis jirovecii. The earliest mode of sexual reproduction among eukaryotes was likely homothallism, that is, self-fertile unisexual reproduction.
Other sexual processes
Besides regular sexual reproduction with meiosis, certain fungi, such as those in the genera Penicillium and Aspergillus, 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. It is known to play a role in intraspecific hybridization and is likely required for hybridization between species, which has been associated with major events in fungal evolution.
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 2,400 million years ago (Ma); these multicellular benthic organisms had filamentous structures capable of anastomosis. Other studies (2009) 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. The oldest fossilizied mycelium to be identified from its molecular composition is between 715 and 810 million years old. For much of the Paleozoic Era (542–251 Ma), 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. Studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.
In May 2019, scientists reported the discovery of a fossilized fungus, named Ourasphaira giraldae, in the Canadian Arctic, that may have grown on land a billion years ago, well before plants were living on land. Pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) have been reported in South China. Earlier, it had been presumed that the fungi colonized the land during the Cambrian (542–488.3 Ma), also long before land plants. Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460 Ma) 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 and early Devonian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–359.2 Ma), 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 (Pennsylvanian, 318.1–299 Ma).
Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 415 Ma; this date roughly 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 (a taxon roughly equivalent to the mushroom-producing species of the Agaricomycetes). Two amber-preserved specimens provide evidence that the earliest known mushroom-forming fungi (the extinct species Archaeomarasmius leggetti) appeared during the late Cretaceous, 90 Ma.
Some time after the Permian–Triassic extinction event (251.4 Ma), a fungal spike (originally thought to be an extraordinary abundance of fungal spores in sediments) 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.
Sixty-five million years ago, immediately after the Cretaceous–Paleogene extinction event that famously killed off most dinosaurs, there was a dramatic increase in evidence of fungi; apparently the death of most plant and animal species led to a huge fungal bloom like "a massive compost heap".
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 fungi. The taxonomy of fungi is in a state of constant flux, especially due to 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. Until relatively recent (2012) changes to the International Code of Nomenclature for algae, fungi and plants, fungal species could also have multiple scientific names depending on their life cycle and mode (sexual or asexual) of reproduction. Web sites such as Index Fungorum and MycoBank are officially recognized nomenclatural repositories and list current names of fungal species (with cross-references to older synonyms).
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, "The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research" and Tedersoo et al. 2018. The lengths of the branches are not proportional to evolutionary distances.
The major phyla (sometimes called divisions) of fungi have been classified mainly on the basis of characteristics of their sexual reproductive structures. As of 2019, nine major lineages have been identified: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycotina, Mucoromycota, 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 (living within the tissue of another species). Previously considered to be "primitive" protozoa, they are now thought to be either a basal branch of the Fungi, or a sister group–each other's closest evolutionary relative.
The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide. Chytrids and their close relatives Neocallimastigomycota and Blastocladiomycota (below) 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. Molecular data and ultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basidiomycota). 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 Chytridiomycota. 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 (e.g., domestic waste landfill sites). They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As in the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.
Microscopic view of a layer of translucent grayish cells, some containing small dark-color spheres
Arbuscular mycorrhiza seen under microscope. Flax root cortical cells containing paired arbuscules.
Cross-section of a cup-shaped structure showing locations of developing meiotic asci (upper edge of cup, left side, arrows pointing to two gray cells containing four and two small circles), sterile hyphae (upper edge of cup, right side, arrows pointing to white cells with a single small circle in them), and mature asci (upper edge of cup, pointing to two gray cells with eight small circles in them)
Diagram of an apothecium (the typical cup-like reproductive structure of Ascomycetes) showing sterile tissues as well as developing and mature asci.
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 (commonly known as 'sugar' and 'pin' molds), 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 (Rhizopus stolonifer), 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 (e.g., of the genera Saccharomyces, Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), 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 (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 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.
Fungus-like organisms
Because of similarities in morphology and lifestyle, the slime molds (mycetozoans, plasmodiophorids, acrasids, Fonticula and labyrinthulids, now in Amoebozoa, Rhizaria, Excavata, Opisthokonta and Stramenopiles, respectively), water molds (oomycetes) and hyphochytrids (both Stramenopiles) were formerly classified in the kingdom Fungi, in groups like Mastigomycotina, Gymnomycota and Phycomycetes. The slime molds were studied also as protozoans, leading to an ambiregnal, duplicated taxonomy.
Unlike true fungi, the cell walls of oomycetes contain cellulose and lack chitin. Hyphochytrids have both chitin and cellulose. Slime molds lack a cell wall during the assimilative phase (except labyrinthulids, which have a wall of scales), and take in nutrients by ingestion (phagocytosis, except labyrinthulids) rather than absorption (osmotrophy, as fungi, labyrinthulids, oomycetes and hyphochytrids). 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 Eccrinales and Amoebidiales are opisthokont protists, previously thought to be zygomycete fungi. Other groups now in Opisthokonta (e.g., Corallochytrium, Ichthyosporea) were also at given time classified as fungi. The genus Blastocystis, now in Stramenopiles, was originally classified as a yeast. Ellobiopsis, now in Alveolata, was considered a chytrid. The bacteria were also included in fungi in some classifications, as the group Schizomycetes.
The Rozellida clade, including the "ex-chytrid" Rozella, is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi. Members of the group that have been isolated lack the chitinous cell wall that is characteristic of fungi. Alternatively, Rozella can be classified as a basal fungal group.
The nucleariids may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom. Many Actinomycetales (Actinomycetota), a group with many filamentous bacteria, were also long believed to be fungi.
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.
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 mycorrhizal relationships with fungi and are dependent upon this relationship for survival.
A microscopic view of blue-stained cells, some with dark wavy lines in them
The dark filaments are hyphae of the endophytic fungus Epichloë coenophiala in the intercellular spaces of tall fescue leaf sheath tissue
The mycorrhizal symbiosis is ancient, dating back to at least 400 million years. 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. The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks". A special case of mycorrhiza is myco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont. Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes. Similar to mycorrhiza, endophytic colonization by fungi may benefit both symbionts; for example, endophytes of grasses impart to their host increased resistance to herbivores and other environmental stresses and receive food and shelter from the plant in return.
With algae and cyanobacteria
A green, leaf-like structure attached to a tree, with a pattern of ridges and depression on the bottom surface
The lichen Lobaria pulmonaria, a symbiosis of fungal, algal, and cyanobacterial species
Lichens are a symbiotic relationship between fungi and photosynthetic algae or cyanobacteria. The photosynthetic partner in the relationship is referred to in lichen terminology as a "photobiont". The fungal part of the relationship is composed mostly of various species of ascomycetes and a few basidiomycetes. Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession, and are prominent in some 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 to the fungus, while the fungus provides minerals and water to the photobiont. 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. Lichenization is a common mode of nutrition for fungi; around 27% of known fungi—more than 19,400 species—are lichenized. Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of desiccation than most other photosynthetic organisms in the same habitat.
With insects
Many insects also engage in mutualistic relationships with fungi. Several groups of ants cultivate fungi in the order Chaetothyriales for several purposes: as a food source, as a structural component of their nests, and as a part of an ant/plant symbiosis in the domatia (tiny chambers in plants that house arthropods). Ambrosia beetles cultivate various species of fungi in the bark of trees that they infest. Likewise, 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. At least one species of stingless bee has a relationship with a fungus in the genus Monascus, where the larvae consume and depend on fungus transferred from old to new nests. 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. Fungi growing in dead wood are essential for xylophagous insects (e.g. woodboring beetles). They deliver nutrients needed by xylophages to nutritionally scarce dead wood. Thanks to this nutritional enrichment the larvae of the woodboring insect is able to grow and develop to adulthood. The larvae of many families of fungicolous flies, particularly those within the superfamily Sciaroidea such as the Mycetophilidae and some Keroplatidae feed on fungal fruiting bodies and sterile mycorrhizae.
A thin brown stick positioned horizontally with roughly two dozen clustered orange-red leaves originating from a single point in the middle of the stick. These orange leaves are three to four times larger than the few other green leaves growing out of the stick, and are covered on the lower leaf surface with hundreds of tiny bumps. The background shows the green leaves and branches of neighboring shrubs.
The plant pathogen Puccinia magellanicum (calafate rust) causes the defect known as witch's broom, seen here on a barberry shrub in Chile.
Gram stain of Candida albicans from a vaginal swab from a woman with candidiasis, showing hyphae, and chlamydospores, which are 2–4 µm in diameter.
Many fungi are parasites on plants, animals (including humans), and other fungi. Serious pathogens of many cultivated plants causing extensive damage and losses to agriculture and forestry include the rice blast fungus Magnaporthe oryzae, tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease, Cryphonectria parasitica responsible for chestnut blight, and Phymatotrichopsis omnivora causing Texas Root Rot, and plant pathogens in the genera Fusarium, Ustilago, Alternaria, and Cochliobolus. Some carnivorous fungi, like Paecilomyces lilacinus, are predators of nematodes, which they capture using an array of specialized structures such as constricting rings or adhesive nets. Many fungi that are plant pathogens, such as Magnaporthe oryzae, can switch from being biotrophic (parasitic on living plants) to being necrotrophic (feeding on the dead tissues of plants they have killed). This same principle is applied to fungi-feeding parasites, including Asterotremella albida, which feeds on the fruit bodies of other fungi both while they are living and after they are dead.
Some fungi can cause serious diseases in humans, several of which may be fatal if untreated. These include aspergillosis, candidiasis, coccidioidomycosis, cryptococcosis, histoplasmosis, mycetomas, and paracoccidioidomycosis. Furthermore, persons with immuno-deficiencies are particularly susceptible to disease by genera such as Aspergillus, Candida, Cryptoccocus, Histoplasma, and Pneumocystis. Other fungi can attack eyes, nails, hair, and especially skin, the so-called dermatophytic and keratinophilic fungi, and cause local infections such as ringworm and athlete's foot. Fungal spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic reactions.
As targets of mycoparasites
Organisms that parasitize fungi are known as mycoparasitic organisms. About 300 species of fungi and fungus-like organisms, belonging to 13 classes and 113 genera, are used as biocontrol agents against plant fungal diseases. Fungi can also act as mycoparasites or antagonists of other fungi, such as Hypomyces chrysospermus, which grows on bolete mushrooms. Fungi can also become the target of infection by mycoviruses.
Communication
Main article: Mycorrhizal networks
There appears to be electrical communication between fungi in word-like components according to spiking characteristics.
Possible impact on climate
According to a study published in the academic journal Current Biology, fungi can soak from the atmosphere around 36% of global fossil fuel greenhouse gas emissions.
Mycotoxins
(6aR,9R)-N-((2R,5S,10aS,10bS)-5-benzyl-10b-hydroxy-2-methyl-3,6-dioxooctahydro-2H-oxazolo[3,2-a] pyrrolo[2,1-c]pyrazin-2-yl)-7-methyl-4,6,6a,7,8,9-hexahydroindolo[4,3-fg] quinoline-9-carboxamide
Ergotamine, a major mycotoxin produced by Claviceps species, which if ingested can cause gangrene, convulsions, and hallucinations
Many fungi produce biologically active compounds, several of which are toxic to animals or plants and are therefore called mycotoxins. Of particular relevance to humans are mycotoxins produced by molds causing food spoilage, and poisonous mushrooms (see above). Particularly infamous are the lethal amatoxins in some Amanita mushrooms, and ergot alkaloids, which have a long history of causing serious epidemics of ergotism (St Anthony's Fire) in people consuming rye or related cereals contaminated with sclerotia of the ergot fungus, Claviceps purpurea. Other notable mycotoxins include the aflatoxins, which are insidious liver toxins and highly carcinogenic metabolites produced by certain Aspergillus species often growing in or on grains and nuts consumed by humans, ochratoxins, patulin, and trichothecenes (e.g., T-2 mycotoxin) and fumonisins, which have significant impact on human food supplies or animal livestock.
Mycotoxins are secondary metabolites (or natural products), and research has established the existence of biochemical pathways solely for the purpose of producing mycotoxins and other natural products in fungi. Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory). Many fungal secondary metabolites (or derivatives) are used medically, as described under Human use below.
Pathogenic mechanisms
Ustilago maydis is a pathogenic plant fungus that causes smut disease in maize and teosinte. Plants have evolved efficient defense systems against pathogenic microbes such as U. maydis. A rapid defense reaction after pathogen attack is the oxidative burst where the plant produces reactive oxygen species at the site of the attempted invasion. U. maydis can respond to the oxidative burst with an oxidative stress response, regulated by the gene YAP1. The response protects U. maydis from the host defense, and is necessary for the pathogen's virulence. Furthermore, U. maydis has a well-established recombinational DNA repair system which acts during mitosis and meiosis. The system may assist the pathogen in surviving DNA damage arising from the host plant's oxidative defensive response to infection.
Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals. C. neoformans usually infects the lungs, where it is phagocytosed by alveolar macrophages. Some C. neoformans can survive inside macrophages, which appears to be the basis for latency, disseminated disease, and resistance to antifungal agents. One mechanism by which C. neoformans survives the hostile macrophage environment is by up-regulating the expression of genes involved in the oxidative stress response. Another mechanism involves meiosis. The majority of C. neoformans are mating "type a". Filaments of mating "type a" ordinarily have haploid nuclei, but they can become diploid (perhaps by endoduplication or by stimulated nuclear fusion) to form blastospores. The diploid nuclei of blastospores can undergo meiosis, including recombination, to form haploid basidiospores that can be dispersed. This process is referred to as monokaryotic fruiting. This process requires a gene called DMC1, which is a conserved homologue of genes recA in bacteria and RAD51 in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus, C. neoformans can undergo a meiosis, monokaryotic fruiting, that promotes recombinational repair in the oxidative, DNA damaging environment of the host macrophage, and the repair capability may contribute to its virulence.
Human use
See also: Human interactions with fungi
Microscopic view of five spherical structures; one of the spheres is considerably smaller than the rest and attached to one of the larger spheres
Saccharomyces cerevisiae cells shown with DIC microscopy
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. 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. Fungi-based industries are sometimes considered to be a major part of a growing bioeconomy, with applications under research and development including use for textiles, meat substitution and general fungal biotechnology.
Therapeutic uses
Modern chemotherapeutics
Many species produce metabolites that are major sources of pharmacologically active drugs.
Antibiotics
Particularly important are the antibiotics, including the penicillins, a structurally related group of β-lactam antibiotics that are synthesized from small peptides. Although naturally occurring penicillins such as penicillin G (produced by Penicillium chrysogenum) have a relatively narrow spectrum of biological activity, a wide range of other penicillins can be produced by chemical modification of the natural penicillins. Modern penicillins are semisynthetic compounds, obtained initially from fermentation cultures, but then structurally altered for specific desirable properties. Other antibiotics produced by fungi include: ciclosporin, commonly used as an immunosuppressant during transplant surgery; and fusidic acid, used to help control infection from methicillin-resistant Staphylococcus aureus bacteria. Widespread use of antibiotics for the treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and others began in the early 20th century and continues to date. In nature, antibiotics of fungal or bacterial origin appear to play a dual role: at high concentrations they act as chemical defense against competition with other microorganisms in species-rich environments, such as the rhizosphere, and at low concentrations as quorum-sensing molecules for intra- or interspecies signaling.
Other
Other drugs produced by fungi include griseofulvin isolated from Penicillium griseofulvum, used to treat fungal infections, and statins (HMG-CoA reductase inhibitors), used to inhibit cholesterol synthesis. Examples of statins found in fungi include mevastatin from Penicillium citrinum and lovastatin from Aspergillus terreus and the oyster mushroom. Psilocybin from fungi is investigated for therapeutic use and appears to cause global increases in brain network integration. Fungi produce compounds that inhibit viruses and cancer cells. Specific metabolites, such as polysaccharide-K, ergotamine, and β-lactam antibiotics, are routinely used in clinical medicine. The shiitake mushroom is a source of lentinan, a clinical drug approved for use in cancer treatments in several countries, including Japan. In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from Trametes versicolor, is an approved adjuvant for cancer therapy.
Traditional medicine
Upper surface view of a kidney-shaped fungus, brownish-red with a lighter yellow-brown margin, and a somewhat varnished or shiny appearance
Two dried yellow-orange caterpillars, one with a curly grayish fungus growing out of one of its ends. The grayish fungus is roughly equal to or slightly greater in length than the caterpillar, and tapers in thickness to a narrow end.
The fungi Ganoderma lucidum (left) and Ophiocordyceps sinensis (right) are used in traditional medicine practices
Certain mushrooms are used as supposed therapeutics in folk medicine practices, such as traditional Chinese medicine. Mushrooms with a history of such use include Agaricus subrufescens, Ganoderma lucidum, and Ophiocordyceps sinensis.
Cultured foods
Baker's yeast or Saccharomyces cerevisiae, a unicellular fungus, is used to make bread and other wheat-based products, such as pizza dough and dumplings. Yeast species of the genus Saccharomyces are also used to produce alcoholic beverages through fermentation. Shoyu koji mold (Aspergillus oryzae) is an essential ingredient in brewing Shoyu (soy sauce) and sake, and the preparation of miso while Rhizopus species are used for making tempeh. Several of these fungi are domesticated species that were bred or selected according to their capacity to ferment food without producing harmful mycotoxins (see below), which are produced by very closely related Aspergilli. Quorn, a meat substitute, is made from Fusarium venenatum.
As the wort boils, the fermenter is carved. Again, the innards are retained and sifted through for pumpkin seeds.
The conicals are reading 36* and 37*, and the glycol is at 25*. This setup allows me to crash the conicals and fine the beers right in the fermentor.
Four days after the beer was brewed, the fermenter's lid fell in due to natural decay of the fermenter. Not all that surprising, but this is not a good state of affairs, as it leaves the fermenting beer exposed to tasty beer-unfriendly microorganisms like bacteria and wild yeasts. Note plastic control fermenter at right; its lid did not fall in.
The inside of my new Morebeer domed conical lid. A 1.5" ferrule was added for my thermowell. A 1.5" cap was drilled and the thermowell welded into place.
The glycol is so cold this picture shows frost developing on the coolant supply line while crashing the beer.
Such a pretty copper color. Changing leaves, beer, pumpkins; fall isn't just in the air. The starting gravity of the wort (i.e., the amount of sugars and particulate matter in the wort -- water has a specific gravity of 1.000) was 1.042, making it a fairly light beer.
#FERMENT, my site specific project for #HYPERsculptures @lightart_museum opening 4 November 22 and running through 30 April 23. Incredible museum with site specific installations by Rebecca Horn, @jamesturell , @studioolafureliasson , @keith_sonnier and many others including @squidie
Here is the transfer from conical to keg. It is a closed transfer from the fermentor into a purged keg. The scale lets me know when the keg is full without needing to have the lid open.
After 36 hours the krausen is thicker still and is starting to look a lot cleaner; the action of the yeast is causing the wort proteins to sink down to the bottom of the carboy.
The manifold has slits cut into the bottom of each tube, allowing the sugar-rich wort to be drained off the spent grain.
#FERMENT, my site specific project for #HYPERsculptures @lightart_museum opening 4 November 22 and running through 30 April 23. Incredible museum with site specific installations by Rebecca Horn, @jamesturell , @studioolafureliasson , @keith_sonnier and many others including @squidie
The sweet wort is slowly drawn off the tun into the kettle. Note that the sparge continues as the wort is run off. Typically, wort is recirculated; recirculation clarifies the wort and draws more sugar out of the grain.
The mash is complete, and now more hot liquor is added to the mash tun. This is done to draw more sugars out of the mash, increase the viscosity of the wort (to better the flow of the run off), and increase the volume of wort to be boiled.
I decided to end this batch after six weeks of fermenting. It has a nice kraut smell, even more than the four week ferment batches. One odd thing, I used a measured shot glass with red dye or ink on the outside of the glass to hold down the cabbage in the Ball mason jars. In the six week ferment, the red ink completely dissolved from the shot glass. I had no idea that could happen. So, I emailed the company hoping the decorative ink/dye/whatever is not toxic to my sauerkraut batch. It tastes fine. After this experiment, I think that I will allow all my future sauerkraut batches to ferment six weeks. It really made a difference in taste in my opinion.
Followup: Next time I will use clear glass items to weigh down my cabbage. Although the company that made these shot glasses said the dye is non-toxic, they also said the acid created by fermentation could dissolve the enamel on the surface of the item. Who knew glass could be so complicated? So, I will be discarding the sauerkraut and making a new batch eventually.
The tap is fit into a hole drilled into the tun. The thick walls of the pumpkin made it difficult to connect the manifold to the tap.
I went to the Real Ale Brewery for their Friday tasting. I took a bunch of pictures and for some reason this is my favorite - the one of the ceiling. Who knows...
The plastic fermenter performed admirably, with no decay or fallen-in lid.
The beer coming out was crystal clear, very dry and hoppy.
Making mead for the second time. Here's a brief history on the "nectar of the gods"...
"The history of mead may go back more than 8,000 years. The oldest known meads were created on the Island of Crete. Wine had not yet been created. Mead was the drink of the Age of Gold, and the word for drunk in classical Greek remained "honey-intoxicated."
Polish mead produced in LublinMead was once very popular in Northern Europe, often produced by monks in monasteries in areas where grapes could not be grown. It faded in popularity, however, once wine imports became economical. Especially partial to it were the Slavs. In Polish it is called miód pitny (pronounced [mjut pi:tni]), meaning "drinkable honey". Mead was a favored drink among the Polish-Lithuanian szlachta (nobility). During the Crusades, Polish Prince Leszek I the White explained to the Pope that Polish knights could not participate in the Crusades because there was no mead in Palestine.
In Norse mythology, mead was the favorite drink of the Norse gods and heroes, e.g. in Valhalla, and the mead of the giant (Jotun) Suttung, made from the blood of Kvasir, was the source of wisdom and poetry. The nectar and ambrosia of the Greek gods are often thought of as draughts of fermented honey.
In Russia, mead remained popular as medovukha and sbiten long after its popularity declined in the West. Sbiten is often mentioned in the works by 19th-century Russian writers, including Gogol, Dostoevsky, and Tolstoy. Some beer producers attempt to revive sbiten' as a mass-produced drink in Russia.
In Finland, a sweet mead called Sima (cognate with zymurgy), is still an essential seasonal brew connected with the Finnish Vappu (May Day) festival. It is usually spiced by adding both the pulp and rind of a lemon. During secondary fermentation raisins are added to control the amount of sugars and to act as an indicator of readiness for consumption — they will rise to the top of the bottle when the drink is ready.
Ethiopian mead is called tej and is usually home-made. It is flavored with the powdered leaves and bark of gesho, a hops-like bittering agent which is a species of buckthorn. A sweeter, less-alcoholic version called berz, aged for a shorter time, is also made. The traditional vessel for drinking tej is a rounded vase-shaped container called a berele.
Evidence exists that mead was also made in India, Southeast Asia, China, Japan, and Central Africa. Mead is also mentioned in many old north Anglo-Saxon stories, including in the epic poem Beowulf, and in early Welsh poetry such as Y Gododdin.
The word "honeymoon" in English is supposedly traceable to the practice of a bride's father dowering her with enough mead for a month-long celebration in honor of the marriage. Mead is still manufactured in Britain, France, and various other locations, though the traditional status of most such manufacture is dubious. One of the most famous producers is the Holy Island of Lindisfarne in North East England, where mead has been produced since Anglo-Saxon times.
Varieties of mead
Mead can have a wide range of flavors, depending on the source of the honey, additives called "adjuncts" or "gruit" (including fruit and spices), yeast employed during fermentation, and aging procedure. Mead can be difficult to find commercially, though some producers have been successful marketing it. Consumers must bear in mind that some producers have marketed white wine with added honey as mead, often spelling it "meade." Blended varieties of mead can be known by either style represented. For instance, a mead made with cinnamon and apples can be referred to as a cinnamon cyser or as an apple metheglin.
Some meads retain some measure of the sweetness of the original honey, and some can even be considered as dessert wines. Drier meads are also available, and some producers offer sparkling meads, which (like champagne) can make for a delightful celebratory toast. There are a number of faux-meads, which are actually cheap wines with large amounts of honey added, to produce a cloyingly sweet liqueur. It has been said that "a mead that tastes of honey is as good as a wine that still tastes of grape".
Historically, meads would have been fermented by wild yeasts and bacteria [citation needed] residing on the skins of the fruit or within the honey itself. Wild yeasts generally provide inconsistent results, and in modern times various brewing interests have isolated the strains now in use. Certain strains have gradually become associated with certain styles of mead. Mostly, these are strains that are also used in beer or wine production. Several commercial labs, such as White Labs, WYeast, Vierka, and others have gone so far as to develop strains specifically for mead.
Mead can also be distilled to a brandy or liqueur strength. Krupnik is a sweet Polish liqueur made through just such a process.
Different types of mead include, but are not limited to:
Braggot - Braggot (also called bracket or brackett) marks the invention of Ale. Originally brewed with honey and hops, later with honey and malt - with or without hops added.
Black mead - A name sometimes given to the blend of honey and black currants.
Cyser - Cyser is a blend of honey and apple juice fermented together. See also cider.
Great mead - Any mead that is intended to be aged several years, like vintage wine. The designation is meant to distinguish this type of mead from "short mead" (see below.)
Hydromel - Hydromel literally means "water-honey" in Greek. It is also the French name for mead. (Compare with the Spanish hidromiel and aquamiel, Italian idromele and Portuguese hidromel). It is also used as a name for a very light or low-alcohol mead.
Melomel - Melomel is made from honey and any fruit. Depending on the fruit-base used, certain melomels may also be known by more specific names (see cyser, pyment, morat for examples)
Metheglin - Metheglin starts with traditional mead but has herbs and spices added. Some of the most common metheglins are ginger, tea, orange peel, coriander, cinnamon, cloves, or vanilla. Its name indicates that many metheglins were originally employed as folk medicines. (Though the Welsh word for honey is medd, the word "metheglin" actually derives from meddeglyn, a compound word comprised of meddyg, "healing" + llyn, "liquor".)
Morat - Morat blends honey and mulberries.
Omphacomel - A medieval mead recipe that blends honey with verjuice; could therefore be considered a variety of pyment.
Oxymel - Another historical mead recipe, blending honey with wine vinegar.
Perry - Perry-mead blends honey with milled, ripe pears. (See entry for the modern drink Babycham.)
Pyment - Pyment blends honey and red or white grapes. Pyment made with white grape juice is sometimes called "white mead."
Rhodomel - Rhodomel is made from honey, rose hips, petals, or rose attar, and water.
Sack mead - This refers to mead that is made with more copious amounts of honey than usual. The finished product retains an extremely high specific gravity and elevated levels of sweetness. It derives its name from the fortified dessert wine Sherry (which is sometimes sweetened after fermentation, and in England once bore the nickname of "sack".)
Short mead - Also called "quick mead". A type of mead recipe that is meant to age quickly, for immediate consumption. Because of the techniques used in its creation, short mead shares some qualities found in cider (or even light ale): primarily that it is effervescent, and often has a cidery taste.[citation needed]
Show mead - A term which has come to mean "plain" mead; that which has honey and water as a base, with no fruits, spices or extra flavorings. (Since honey alone does not provide enough nourishment for the yeast to carry on its life-cycle, a mead that is devoid of fruit, etc. will require a special yeast nutrient and other enzymes to produce an acceptable finished product.)
Tej - Tej is an Ethiopian mead, fermented with wild yeasts (and bacteria), and with the addition of gesho. Recipes vary from family to family, with some recipes leaning towards braggot with the inclusion of grains.
Mulsum - Mulsum is not a true mead, but is unfermented honey blended with a high-alcohol wine.
Medovina - Macedonian (of the Republic of Macedonia) for mead. Unfortunately, very few people still brew this for their own consumption. It is not available commercially.
Medovukha - Eastern Slavic variant, very alcoholic. In principle, a vodka with distilled honey addition.
Półtorak - A Polish mead, made using two units of honey for each unit of water
Dwójniak - A Polish mead, made using equal amounts of water and honey
Trójniak - A Polish mead, made using two units of water for each unit of honey
Czwórniak - A Polish mead, made using three units of water for each unit of honey
Gverc or Medovina - Croatian mead prepared in Samobor and many other places. Word “gverc” or “gvirc” is from German "Gewürze" and it refers to different spices added to mead."
The initial hop addition is for bittering. More hops are added halfway through the boil for flavoring. A final addition at the end of the boil boosts the aroma.
I'm always on the hunt for something new. When I went to Trader Joe's today I didn't expect to find this product. It's new and I know it sounds weird, but I tasted some and The garlic cloves are black, not very appetizing in appearance, however, "WOW!" My taste buds say it's like eating a tangy fig and date combined!!! Who would have thought garlic could taste like this. I know when you cook garlic that heavy flavour goes away, but this is not like that, fermenting does a whole different thing to it!
Boiling accomplishes a number of things: microorganisms in the wort are killed off, alpha acids and other components in the hops are drawn into the wort, and the volume of the wort is reduced.
The boil is complete and wort is pumped from the kettle through chillers into a sanitized bucket. After passing through the chillers, the wort's temperature is approximately 70 degrees Farenheit. Chilling makes it possible to immediately inoculate the wort with yeast and reduce the possibility of a bacterial infection.
Time passes as the mash progresses. Inside the pumpkin, enzymes in the barley -- activated by the addition of the hot liquor -- are converting the complex sugars in the grain into simple sugars. The tun is closed up to retain heat.
The tap was removed after the majority of the wort ran off. Some wort continued to run off. The visual effect is vaguely obscene.
A friend of Jersey Shore Fightin’ Texas Aggie Ring gave him a gallon-sized container of pealed fresh garlic imported from Spain. It’s delicious. As much as Aggie Ring uses garlic, there’s no way he can use that much before it turns. Aggie Ring implemented “Operation Ferment Garlic” to prevent wasting it.
Aggie Ring took the garlic, cut off the end where it connected to the root (?) or plant (?) [perhaps it’s both?] and then had me lightly “smash” it (just enough to break each clove a bit) with the palm of my “Aggie Ring Hand.”
“Aggie Ring Hand?” is what you gentle readers are probably thinking. Let me explain. When I was blessed with my first Texas A&M University Fightin’ Texas Aggie Ring, he was a “right hand” Texas Aggie Ring. This was back in the mid-1980s and there were still several of my professors and staff at Texas A&M who were WW II veterans and alumni from the 1940s and 1950s.
In fact, the professor who was my undergraduate and graduate student advisor in the college of engineering was class of 1954. He had been in the Fightin’ Texas Aggie Band when he’d been a student and played the clarinet. He still could play the War Hymn every year when the Aggie Band had this thing where the old BQ (Band Qualified) alumni would march from the Quad to Kyle Field for a game with just the Aggie football team playing against each other.
Anyway. I got so much crap from a number of those Old Ags for wearing my ring on my right hand that I felt the need as a real Texas Aggie to switch Aggie Ring ’84 over to my left. Evidently, only girls should wear their Aggie Rings on their right hand. Also, it was a time-honored tradition that a man wears his Aggie Ring on his left hand because the left hand is closer to the heart and, if you’re married, it shows your spouse that you love them as much as you love Texas A&M. I remember seeing a number of Old Ags who had taken their wedding bands and had them “bound” (if that’s the correct term) to their Aggie Ring. “Sweet” said Aggie Ring ’84. “I want to be a left-handed Aggie Ring like an old-school Aggie Ring.”
To this day, when Fightin’ Texas A&M Aggie Ring ’84 sees a photo of a young Aggie wearing his or her ring on their left hand (the proper Aggie hand), he smiles just a little bit brighter.
So, Aggie Ring had me lightly “crush” the garlic cloves and put them into the Ball jar. Once the Ball jar was full of garlic up to just below the lip, Aggie Ring took raw unfiltered honey (it has to be raw!) and poured it into the jar until all of the garlic was covered. This took about an hour as the honey moves slowly.
You can see how much of the 24 oz bottle of raw honey it took in the photo. Aggie Ring put a fermentation lid he bought a bunch of on Amazon on the jar but if someone doesn’t have one, they can just put a lid on loosely or “burp” the jar every couple of days. You don’t want to put the lid on tightly and leave it because the jar will eventually explode.
The wild yeast that is present on the garlic cause the chemical reaction that causes the fermentation. Honey ferments slowly, so it takes about three weeks or more for everything to process.
Now, Aggie Ring has done this before and the finished product is incredible. The honey gets thinner like pancake syrup because of the alcohol that’s produced in the fermentation process. It’s delicious drizzled over pizza. Yes, that’s a thing. Aggie Ring has been to a pizza parlor in Kansas City where there’s a honey bear on every table. People who go there pour honey all over their slices of pie. Aggie Ring hasn’t experimented yet, but he strongly suspects that honey might taste good on some BBQ brisket. It’s certainly healthier than that high fructose corn syrup BBQ sauce most people use. The fermentation and the sweetness of the honey kills off that nasty garlic “bite” and that garlic is incredible on a salad or in pretty much anything (soups, beans, chili… etc.).
As I mentioned, Aggie Ring had me use my Aggie Ring Hand to crush/bruise all of those cloves of garlic. After crushing all of those cloves, my hand smelled like a garlic field. As much as Aggie Ring ’84 doesn’t like vampires, he didn’t want my proper Aggie Ring Hand [the left] to smell like a field of garlic plants for days. :-)
Luckily, someone had recently sent us a stainless steel bar of “soap” that claimed that if you wash your hands with it just like a regular bar of soap, it will kill the smell of onions or garlic on your hands. Aggie Ring took a leap of faith.
It worked. It totally killed the smell of garlic on my proper Aggie Ring Hand [left]. This thing is incredible. I think they are only around $5.00 on Amazon.
Now, all the Aggie Ring and I have to do is wait a few weeks for the garlic to ferment. “Patience grasshopper.” Aggie Ring told me. “It will be done when it is done. Not before.”
#AggieRing
“The road goes on forever and the party never ends.” — Aggie Ring
Got a pork loin and a belly for this batch instead of pork shoulder. I'm hoping to get a better blend of meat and fat. Fermenting using the starter culture I have should take around 48 hours at 65-75 degF, with a pan of water in the bottom of the oven to keep the humidity near 80%.I use the oven because it is a draft free environment. Curing and drying will take around 4 weeks to reach 35-40% weight loss.