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The animal kingdom is filled up to the point we sometimes think that we have to many. Well we don't we actually need them without them than we wouldn't have the food chain. Did you know that there are 1.2 million different species of animals that we known.

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Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia (). With few exceptions, animals consume organic material, breathe oxygen, have myocytes and are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Animals form a clade, meaning that they arose from a single common ancestor.

Over 1.5 million living animal species have been described, of which around 1.05 million are insects, over 85,000 are molluscs, and around 65,000 are vertebrates. It has been estimated there are as many as 7.77 million animal species on Earth. Animal body lengths range from 8.5 μm (0.00033 in) to 33.6 m (110 ft). They have complex ecologies and interactions with each other and their environments, forming intricate food webs. The scientific study of animals is known as zoology, and the study of animal behaviors is known as ethology.

Most living animal species belong to the infrakingdom Bilateria, a highly proliferative clade whose members have a bilaterally symmetric body plan. The vast majority belong to two large superphyla: the protostomes, which includes organisms such as the arthropods, molluscs, flatworms, annelids and nematodes; and the deuterostomes, which include the echinoderms, hemichordates and chordates, the latter of which contains the vertebrates. The simple Xenacoelomorpha have an uncertain position within Bilateria.

Animals first appear in the fossil record in the late Cryogenian period, and diversified in the subsequent Ediacaran. Earlier evidence of animals is still controversial; the sponge-like organism has been dated back to the Tonian period at the start of the Neoproterozoic, but its identity as an animal is heavily contested. Nearly all modern animal phyla became clearly established in the fossil record as marine species during the Cambrian explosion, which began around 539 million years ago (Mya), and most classes during the Ordovician radiation 485.4 Mya. 6,331 groups of genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived about 650 Mya during the Cryogenian period.

Historically, Aristotle divided animals into those with blood and those without. Carl Linnaeus created the first hierarchical biological classification for animals in 1758 with his Systema Naturae, which Jean-Baptiste Lamarck expanded into 14 phyla by 1809. In 1874, Ernst Haeckel divided the animal kingdom into the multicellular Metazoa (now synonymous with Animalia) and the Protozoa, single-celled organisms no longer considered animals. In modern times, the biological classification of animals relies on advanced techniques, such as molecular phylogenetics, which are effective at demonstrating the evolutionary relationships between taxa.

Humans make use of many other animal species for food (including meat, eggs, and dairy products), for materials (such as leather, fur, and wool), as pets and as working animals for transportation, and services. Dogs, the first domesticated animal, have been used in hunting, in security and in warfare, as have horses, pigeons and birds of prey; while other terrestrial and aquatic animals are hunted for sports, trophies or profits. Non-human animals are also an important cultural element of human evolution, having appeared in cave arts and totems since the earliest times, and are frequently featured in mythology, religion, arts, literature, heraldry, politics, and sports.

The word animal comes from the Latin noun animal of the same meaning, which is itself derived from Latin animalis 'having breath or soul'. The biological definition includes all members of the kingdom Animalia. In colloquial usage, the term animal is often used to refer only to nonhuman animals. The term metazoa is derived from Ancient Greek μετα ( meta) 'after' (in biology, the prefix meta- stands for 'later') and ζῷᾰ ( zōia) 'animals', plural of ζῷον zōion 'animal'.

Characteristics

Animals have several characteristics that set them apart from other living things. Animals are eukaryotic and multicellular. Unlike plants and algae, which produce their own nutrients, animals are heterotrophic, feeding on organic material and digesting it internally. With very few exceptions, animals respire aerobically. All animals are motile (able to spontaneously move their bodies) during at least part of their life cycle, but some animals, such as sponges, corals, mussels, and barnacles, later become sessile. The blastula is a stage in embryonic development that is unique to animals, allowing cells to be differentiated into specialised tissues and organs.

All animals are composed of cells, surrounded by a characteristic extracellular matrix composed of collagen and elastic glycoproteins. During development, the animal extracellular matrix forms a relatively flexible framework upon which cells can move about and be reorganised, making the formation of complex structures possible. This may be calcified, forming structures such as shells, bones, and spicules. In contrast, the cells of other multicellular organisms (primarily algae, plants, and fungi) are held in place by cell walls, and so develop by progressive growth. Animal cells uniquely possess the cell junctions called tight junctions, gap junctions, and desmosomes.

With few exceptions-in particular, the sponges and placozoans-animal bodies are differentiated into tissues. These include muscles, which enable locomotion, and nerve tissues, which transmit signals and coordinate the body. Typically, there is also an internal digestive chamber with either one opening (in Ctenophora, Cnidaria, and flatworms) or two openings (in most bilaterians).

Reproduction and development

Nearly all animals make use of some form of sexual reproduction. They produce haploid gametes by meiosis; the smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova. These fuse to form zygotes, which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge. In most other groups, the blastula undergoes more complicated rearrangement. It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm. In most cases, a third germ layer, the mesoderm, also develops between them. These germ layers then differentiate to form tissues and organs.

Repeated instances of mating with a close relative during sexual reproduction generally leads to inbreeding depression within a population due to the increased prevalence of harmful recessive traits. Animals have evolved numerous mechanisms for avoiding close inbreeding.

Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation; budding, such as in Hydra and other cnidarians; or parthenogenesis, where fertile eggs are produced without mating, such as in aphids.

Predators, such as this ultramarine flycatcher (Ficedula superciliaris), feed on other animals.

Animals are categorised into ecological groups depending on their trophic levels and how they consume organic material. Such groupings include carnivores (further divided into subcategories such as piscivores, insectivores, ovivores, etc.), herbivores (subcategorized into folivores, graminivores, frugivores, granivores, nectarivores, algivores, etc.), omnivores, fungivores, scavengers/ detritivores, and parasites. Interactions between animals of each biome form complex food webs within that ecosystem. In carnivorous or omnivorous species, predation is a consumer-resource interaction where the predator feeds on another organism, its prey, who often evolves anti-predator adaptations to avoid being fed upon. Selective pressures imposed on one another lead to an evolutionary arms race between predator and prey, resulting in various antagonistic/ competitive coevolutions. Almost all multicellular predators are animals. Some consumers use multiple methods; for example, in parasitoid wasps, the larvae feed on the hosts' living tissues, killing them in the process, but the adults primarily consume nectar from flowers. Other animals may have very specific feeding behaviours, such as hawksbill sea turtles which mainly eat sponges.

Hydrothermal vent mussels and shrimps

Most animals rely on biomass and bioenergy produced by plants and phytoplanktons (collectively called producers) through photosynthesis. Herbivores, as primary consumers, eat the plant material directly to digest and absorb the nutrients, while carnivores and other animals on higher trophic levels indirectly acquire the nutrients by eating the herbivores or other animals that have eaten the herbivores. Animals oxidize carbohydrates, lipids, proteins and other biomolecules, which allows the animal to grow and to sustain basal metabolism and fuel other biological processes such as locomotion. Some benthic animals living close to hydrothermal vents and cold seeps on the dark sea floor consume organic matter produced through chemosynthesis (via oxidizing inorganic compounds such as hydrogen sulfide) by archaea and bacteria.

Animals evolved in the sea. Lineages of arthropods colonised land around the same time as land plants, probably between 510 and 471 million years ago during the Late Cambrian or Early Ordovician. Vertebrates such as the lobe-finned fish started to move on to land in the late Devonian, about 375 million years ago. Animals occupy virtually all of earth's habitats and microhabitats, with faunas adapted to salt water, hydrothermal vents, fresh water, hot springs, swamps, forests, pastures, deserts, air, and the interiors of other organisms. Animals are however not particularly heat tolerant; very few of them can survive at constant temperatures above 50 °C (122 °F) or in the most extreme cold deserts of continental Antarctica.

The blue whale is the largest animal that has ever lived.

The blue whale ( Balaenoptera musculus) is the largest animal that has ever lived, weighing up to 190 tonnes and measuring up to 33.6 metres (110 ft) long. The largest extant terrestrial animal is the African bush elephant ( Loxodonta africana), weighing up to 12.25 tonnes and measuring up to 10.67 metres (35.0 ft) long. The largest terrestrial animals that ever lived were titanosaur sauropod dinosaurs such as Argentinosaurus, which may have weighed as much as 73 tonnes, and Supersaurus which may have reached 39 meters. Several animals are microscopic; some Myxozoa ( obligate parasites within the Cnidaria) never grow larger than 20 μm, and one of the smallest species ( Myxobolus shekel) is no more than 8.5 μm when fully grown.

Numbers and habitats of major phyla

The following table lists estimated numbers of described extant species for the major animal phyla, along with their principal habitats (terrestrial, fresh water, and marine), and free-living or parasitic ways of life. Species estimates shown here are based on numbers described scientifically; much larger estimates have been calculated based on various means of prediction, and these can vary wildly. For instance, around 25,000-27,000 species of nematodes have been described, while published estimates of the total number of nematode species include 10,000-20,000; 500,000; 10 million; and 100 million. Using patterns within the taxonomic hierarchy, the total number of animal species-including those not yet described-was calculated to be about 7.77 million in 2011.

Evolutionary origin

Evidence of animals is found as long ago as the Cryogenian period. 24-Isopropylcholestane (24-ipc) has been found in rocks from roughly 650 million years ago; it is only produced by sponges and pelagophyte algae. Its likely origin is from sponges based on molecular clock estimates for the origin of 24-ipc production in both groups. Analyses of pelagophyte algae consistently recover a Phanerozoic origin, while analyses of sponges recover a Neoproterozoic origin, consistent with the appearance of 24-ipc in the fossil record.

The first body fossils of animals appear in the Ediacaran, represented by forms such as and . It had long been doubted whether these fossils truly represented animals, but the discovery of the animal lipid cholesterol in fossils of Dickinsonia establishes their nature. Animals are thought to have originated under low-oxygen conditions, suggesting that they were capable of living entirely by anaerobic respiration, but as they became specialized for aerobic metabolism they became fully dependent on oxygen in their environments.

Many animal phyla first appear in the fossil record during the Cambrian explosion, starting about 539 million years ago, in beds such as the Burgess shale. Extant phyla in these rocks include molluscs, brachiopods, onychophorans, tardigrades, arthropods, echinoderms and hemichordates, along with numerous now-extinct forms such as the predatory Anomalocaris. The apparent suddenness of the event may however be an artifact of the fossil record, rather than showing that all these animals appeared simultaneously. That view is supported by the discovery of Auroralumina attenboroughii, the earliest known Ediacaran crown-group cnidarian (557-562 mya, some 20 million years before the Cambrian explosion) from Charnwood Forest, England. It is thought to be one of the earliest predators, catching small prey with its nematocysts as modern cnidarians do.

Some palaeontologists have suggested that animals appeared much earlier than the Cambrian explosion, possibly as early as 1 billion years ago. Early fossils that might represent animals appear for example in the 665-million-year-old rocks of the Trezona Formation of South Australia. These fossils are interpreted as most probably being early sponges. Trace fossils such as tracks and burrows found in the Tonian period (from 1 gya) may indicate the presence of triploblastic worm-like animals, roughly as large (about 5 mm wide) and complex as earthworms. However, similar tracks are produced by the giant single-celled protist Gromia sphaerica, so the Tonian trace fossils may not indicate early animal evolution. Around the same time, the layered mats of microorganisms called stromatolites decreased in diversity, perhaps due to grazing by newly evolved animals. Objects such as sediment-filled tubes that resemble trace fossils of the burrows of wormlike animals have been found in 1.2 gya rocks in North America, in 1.5 gya rocks in Australia and North America, and in 1.7 gya rocks in Australia. Their interpretation as having an animal origin is disputed, as they might be water-escape or other structures.

External phylogeny

Animals are monophyletic, meaning they are derived from a common ancestor. Animals are the sister group to the choanoflagellates, with which they form the Choanozoa. The dates on the phylogenetic tree indicate approximately how many millions of years ago ( mya) the lineages split.

Ros-Rocher and colleagues (2021) trace the origins of animals to unicellular ancestors, providing the external phylogeny shown in the cladogram. Uncertainty of relationships is indicated with dashed lines.

Internal phylogeny

The most basal animals, the Porifera, Ctenophora, Cnidaria, and Placozoa, have body plans that lack bilateral symmetry. Their relationships are still disputed; the sister group to all other animals could be the Porifera or the Ctenophora, both of which lack hox genes, which are important for body plan development.

Hox genes are found in the Placozoa, Cnidaria, and Bilateria. 6,331 groups of genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived 650 million years ago in the Precambrian. 25 of these are novel core gene groups, found only in animals; of those, 8 are for essential components of the Wnt and TGF-beta signalling pathways which may have enabled animals to become multicellular by providing a pattern for the body's system of axes (in three dimensions), and another 7 are for transcription factors including homeodomain proteins involved in the control of development.

Giribet and Edgecombe (2020) provide what they consider to be a consensus internal phylogeny of the animals, embodying uncertainty about the structure at the base of the tree (dashed lines).

An alternative phylogeny, from Kapli and colleagues (2021), proposes a clade Xenambulacraria for the Xenacoelamorpha + Ambulacraria; this is either within Deuterostomia, as sister to Chordata, or the Deuterostomia are recovered as paraphyletic, and Xenambulacraria is sister to the proposed clade Centroneuralia, consisting of Chordata + Protostomia.

Non-bilateria

Non-bilaterians include sponges (centre) and corals (background).

Several animal phyla lack bilateral symmetry. These are the Porifera (sea sponges), Placozoa, Cnidaria (which includes jellyfish, sea anemones, and corals), and Ctenophora (comb jellies).

Sponges are physically very distinct from other animals, and were long thought to have diverged first, representing the oldest animal phylum and forming a sister clade to all other animals. Despite their morphological dissimilarity with all other animals, genetic evidence suggests sponges may be more closely related to other animals than the comb jellies are. Sponges lack the complex organization found in most other animal phyla; their cells are differentiated, but in most cases not organised into distinct tissues, unlike all other animals. They typically feed by drawing in water through pores, filtering out small particles of food.

The comb jellies and Cnidaria are radially symmetric and have digestive chambers with a single opening, which serves as both mouth and anus. Animals in both phyla have distinct tissues, but these are not organised into discrete organs. They are diploblastic, having only two main germ layers, ectoderm and endoderm.

The tiny placozoans have no permanent digestive chamber and no symmetry; they superficially resemble amoebae. Their phylogeny is poorly defined, and under active research.

Idealised bilaterian body plan.[d] With an elongated body and a direction of movement the animal has head and tail ends. Sense organs and mouth form the basis of the head. Opposed circular and longitudinal muscles enable peristaltic motion.

The remaining animals, the great majority-comprising some 29 phyla and over a million species-form a clade, the Bilateria, which have a bilaterally symmetric body plan. The Bilateria are triploblastic, with three well-developed germ layers, and their tissues form distinct organs. The digestive chamber has two openings, a mouth and an anus, and there is an internal body cavity, a coelom or pseudocoelom. These animals have a head end (anterior) and a tail end (posterior), a back (dorsal) surface and a belly (ventral) surface, and a left and a right side.

Having a front end means that this part of the body encounters stimuli, such as food, favouring cephalisation, the development of a head with sense organs and a mouth. Many bilaterians have a combination of circular muscles that constrict the body, making it longer, and an opposing set of longitudinal muscles, that shorten the body; these enable soft-bodied animals with a hydrostatic skeleton to move by peristalsis. They also have a gut that extends through the basically cylindrical body from mouth to anus. Many bilaterian phyla have primary larvae which swim with cilia and have an apical organ containing sensory cells. However, over evolutionary time, descendant spaces have evolved which have lost one or more of each of these characteristics. For example, adult echinoderms are radially symmetric (unlike their larvae), while some parasitic worms have extremely simplified body structures.

Genetic studies have considerably changed zoologists' understanding of the relationships within the Bilateria. Most appear to belong to two major lineages, the protostomes and the deuterostomes. It is often suggested that the basalmost bilaterians are the Xenacoelomorpha, with all other bilaterians belonging to the subclade Nephrozoa However, this suggestion has been contested, with other studies finding that xenacoelomorphs are more closely related to Ambulacraria than to other bilaterians.

Protostomes and deuterostomes

Protostomes and deuterostomes differ in several ways. Early in development, deuterostome embryos undergo radial cleavage during cell division, while many protostomes (the Spiralia) undergo spiral cleavage. Animals from both groups possess a complete digestive tract, but in protostomes the first opening of the embryonic gut develops into the mouth, and the anus forms secondarily. In deuterostomes, the anus forms first while the mouth develops secondarily. Most protostomes have schizocoelous development, where cells simply fill in the interior of the gastrula to form the mesoderm. In deuterostomes, the mesoderm forms by enterocoelic pouching, through invagination of the endoderm.

The main deuterostome phyla are the Echinodermata and the Chordata. Echinoderms are exclusively marine and include starfish, sea urchins, and sea cucumbers. The chordates are dominated by the vertebrates (animals with backbones), which consist of fishes, amphibians, reptiles, birds, and mammals. The deuterostomes also include the Hemichordata (acorn worms).

Ecdysis: a dragonfly has emerged from its dry exuviae and is expanding its wings. Like other arthropods, its body is divided into segments.

The Ecdysozoa are protostomes, named after their shared trait of ecdysis, growth by moulting. They include the largest animal phylum, the Arthropoda, which contains insects, spiders, crabs, and their kin. All of these have a body divided into repeating segments, typically with paired appendages. Two smaller phyla, the Onychophora and Tardigrada, are close relatives of the arthropods and share these traits. The ecdysozoans also include the Nematoda or roundworms, perhaps the second largest animal phylum. Roundworms are typically microscopic, and occur in nearly every environment where there is water; some are important parasites. Smaller phyla related to them are the Nematomorpha or horsehair worms, and the Kinorhyncha, Priapulida, and Loricifera. These groups have a reduced coelom, called a pseudocoelom.

Spiral cleavage in a sea snail embryo

The Spiralia are a large group of protostomes that develop by spiral cleavage in the early embryo. The Spiralia's phylogeny has been disputed, but it contains a large clade, the superphylum Lophotrochozoa, and smaller groups of phyla such as the Rouphozoa which includes the gastrotrichs and the flatworms. All of these are grouped as the Platytrochozoa, which has a sister group, the Gnathifera, which includes the rotifers.

The Lophotrochozoa includes the molluscs, annelids, brachiopods, nemerteans, bryozoa and entoprocts. The molluscs, the second-largest animal phylum by number of described species, includes snails, clams, and squids, while the annelids are the segmented worms, such as earthworms, lugworms, and leeches. These two groups have long been considered close relatives because they share trochophore larvae.

History of classification

Jean-Baptiste de Lamarck led the creation of a modern classification of invertebrates, breaking up Linnaeus's "Vermes" into 9 phyla by 1809.[168]

In the classical era, Aristotle divided animals, based on his own observations, into those with blood (roughly, the vertebrates) and those without. The animals were then arranged on a scale from man (with blood, 2 legs, rational soul) down through the live-bearing tetrapods (with blood, 4 legs, sensitive soul) and other groups such as crustaceans (no blood, many legs, sensitive soul) down to spontaneously generating creatures like sponges (no blood, no legs, vegetable soul). Aristotle was uncertain whether sponges were animals, which in his system ought to have sensation, appetite, and locomotion, or plants, which did not: he knew that sponges could sense touch, and would contract if about to be pulled off their rocks, but that they were rooted like plants and never moved about.

In 1758, Carl Linnaeus created the first hierarchical classification in his Systema Naturae. In his original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, the Chordata, while his Insecta (which included the crustaceans and arachnids) and Vermes have been renamed or broken up. The process was begun in 1793 by Jean-Baptiste de Lamarck, who called the Vermes une espèce de chaos (a chaotic mess) and split the group into three new phyla: worms, echinoderms, and polyps (which contained corals and jellyfish). By 1809, in his Philosophie Zoologique, Lamarck had created 9 phyla apart from vertebrates (where he still had 4 phyla: mammals, birds, reptiles, and fish) and molluscs, namely cirripedes, annelids, crustaceans, arachnids, insects, worms, radiates, polyps, and infusorians.

In his 1817 Le Règne Animal, Georges Cuvier used comparative anatomy to group the animals into four embranchements ("branches" with different body plans, roughly corresponding to phyla), namely vertebrates, molluscs, articulated animals (arthropods and annelids), and zoophytes (radiata) (echinoderms, cnidaria and other forms). This division into four was followed by the embryologist Karl Ernst von Baer in 1828, the zoologist Louis Agassiz in 1857, and the comparative anatomist Richard Owen in 1860.

In 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms: Metazoa (multicellular animals, with five phyla: coelenterates, echinoderms, articulates, molluscs, and vertebrates) and Protozoa (single-celled animals), including a sixth animal phylum, sponges. The protozoa were later moved to the former kingdom Protista, leaving only the Metazoa as a synonym of Animalia.

In human culture

Practical uses

The human population exploits a large number of other animal species for food, both of domesticated livestock species in animal husbandry and, mainly at sea, by hunting wild species. Marine fish of many species are caught commercially for food. A smaller number of species are farmed commercially. Humans and their livestock make up more than 90% of the biomass of all terrestrial vertebrates, and almost as much as all insects combined.

Invertebrates including cephalopods, crustaceans, and bivalve or gastropod molluscs are hunted or farmed for food. Chickens, cattle, sheep, pigs, and other animals are raised as livestock for meat across the world. Animal fibres such as wool are used to make textiles, while animal sinews have been used as lashings and bindings, and leather is widely used to make shoes and other items. Animals have been hunted and farmed for their fur to make items such as coats and hats. Dyestuffs including carmine ( cochineal), shellac, and kermes have been made from the bodies of insects. Working animals including cattle and horses have been used for work and transport from the first days of agriculture.

Animals such as the fruit fly Drosophila melanogaster serve a major role in science as experimental models. Animals have been used to create vaccines since their discovery in the 18th century. Some medicines such as the cancer drug trabectedin are based on toxins or other molecules of animal origin.

A gun dog retrieving a duck during a hunt

People have used hunting dogs to help chase down and retrieve animals, and birds of prey to catch birds and mammals, while tethered cormorants have been used to catch fish. Poison dart frogs have been used to poison the tips of blowpipe darts. A wide variety of animals are kept as pets, from invertebrates such as tarantulas, octopuses, and praying mantises, reptiles such as snakes and chameleons, and birds including canaries, parakeets, and parrots all finding a place. However, the most kept pet species are mammals, namely dogs, cats, and rabbits. There is a tension between the role of animals as companions to humans, and their existence as individuals with rights of their own.

A wide variety of terrestrial and aquatic animals are hunted for sport.

Symbolic uses

The signs of the Western and Chinese zodiacs are based on animals. In China and Japan, the butterfly has been seen as the personification of a person's soul, and in classical representation the butterfly is also the symbol of the soul.

Artistic vision: Still Life with Lobster and Oysters by Alexander Coosemans, c. 1660

Animals have been the subjects of art from the earliest times, both historical, as in ancient Egypt, and prehistoric, as in the cave paintings at Lascaux. Major animal paintings include Albrecht Dürer's 1515 The Rhinoceros, and George Stubbs's c. 1762 horse portrait Whistlejacket. Insects, birds and mammals play roles in literature and film, such as in giant bug movies.

References

External links

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Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia (). With few exceptions, animals consume organic material, breathe oxygen, have myocytes and are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Animals form a clade, meaning that they arose from a single common ancestor.

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The world is made up of about 29.2% of plants we need plants for pollen and pollen helps bee's make honey and we need honey for food and some medicine there are a lot of plants some useful and some useless.

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Plants

Scientific classification

Domain:

Eukaryota

Clade:

Diaphoretickes

(unranked):

Archaeplastida

Kingdom:

Plantae
H.F.Copel., 1956

Superdivisions

see text

Synonyms

Viridiplantae Cavalier-Smith 1981[1]

Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004[2]

Chlorobiota Kenrick and Crane 1997[3]

Chloroplastida Adl et al., 2005 [4]

Phyta Barkley 1939 emend. Holt & Uidica 2007

Cormophyta Endlicher, 1836

Cormobionta Rothmaler, 1948

Euplanta Barkley, 1949

Telomobionta Takhtajan, 1964

Embryobionta Cronquist et al., 1966

Metaphyta Whittaker, 1969

Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars from carbon dioxide and water, using the green pigment chlorophyll. Exceptions are parasitic plants that have lost the genes for chlorophyll and photosynthesis, and obtain their energy from other plants or fungi.

Historically, as in Aristotle's biology, the plant kingdom encompassed all living things that were not animals, and included algae and fungi. Definitions have narrowed since then; current definitions exclude the fungi and some of the algae. By the definition used in this article, plants form the clade Viridiplantae (green plants), which consists of the green algae and the embryophytes or land plants ( hornworts, liverworts, mosses, lycophytes, ferns, conifers and other gymnosperms, and flowering plants). A definition based on genomes includes the Viridiplantae, along with the red algae and the glaucophytes, in the clade Archaeplastida.

There are about 380,000 known species of plants, of which the majority, some 260,000, produce seeds. They range in size from single cells to the tallest trees. Green plants provide a substantial proportion of the world's molecular oxygen; the sugars they create supply the energy for most of Earth's ecosystems; other organisms, including animals, either consume plants directly or rely on organisms which do so.

Grain, fruit, and vegetables are basic human foods and have been domesticated for millennia. People use plants for many purposes, such as building materials, ornaments, writing materials, and, in great variety, for medicines. The scientific study of plants is known as botany, a branch of biology.

Definition

Taxonomic history

All living things were traditionally placed into one of two groups, plants and animals. This classification dates from Aristotle (384-322 BC), who distinguished different levels of beings in his biology, based on whether living things had a "sensitive soul" or like plants only a "vegetative soul". Theophrastus, Aristotle's student, continued his work in plant taxonomy and classification. Much later, Linnaeus (1707-1778) created the basis of the modern system of scientific classification, but retained the animal and plant kingdoms, naming the plant kingdom the Vegetabilia.

Alternative concepts

When the name Plantae or plant is applied to a specific group of organisms or taxa, it usually refers to one of four concepts. From least to most inclusive, these four groupings are:

Land plants, also known as Embryophyta

Plantae sensu strictissimo

Multicellular

Plants in the strictest sense include liverworts, hornworts, mosses, and vascular plants, as well as fossil plants similar to these surviving groups (e.g., Metaphyta Whittaker, 1969, Plantae Margulis, 1971).

Green plants, also known as Viridiplantae, Viridiphyta, Chlorobionta or Chloroplastida

Plantae sensu stricto

Some unicellular, some multicellular

Plants in a strict sense include the green algae, and land plants that emerged within them, including stoneworts. The relationships between plant groups are still being worked out, and the names given to them vary considerably. The clade Viridiplantae encompasses a group of organisms that have cellulose in their cell walls, possess chlorophylls a and b and have plastids bound by only two membranes that are capable of photosynthesis and of storing starch. This clade is the main subject of this article (e.g., Plantae Copeland, 1956).

Archaeplastida, also known as Plastida or Primoplantae

Plantae sensu lato

Some unicellular, some multicellular

Plants in a broad sense comprise the green plants listed above plus the red algae ( Rhodophyta) and the glaucophyte algae ( Glaucophyta) that store Floridean starch outside the plastids, in the cytoplasm. This clade includes all of the organisms that eons ago acquired their primary chloroplasts directly by engulfing cyanobacteria (e.g., Plantae Cavalier-Smith, 1981).

Old definitions of plant (obsolete)

Plantae sensu amplo

Some unicellular, some multicellular

Plants in the widest sense included the unrelated groups of algae, fungi and bacteria on older, obsolete classifications (e.g. Plantae or Vegetabilia Linnaeus 1751, Plantae Haeckel 1866, Metaphyta Haeckel, 1894, Plantae Whittaker, 1969).

The desmid Cosmarium botrytis is a single cell.

The coast redwood Sequoia sempervirens is up to 380 feet (120 m) tall.

There are about 382,000 accepted species of plants, of which the great majority, some 283,000, produce seeds. The table below shows some species count estimates of different green plant (Viridiplantae) divisions. About 85-90% of all plants are flowering plants. Several projects are currently attempting to collect records on all plant species in online databases, e.g. the World Flora Online.

Plants range in scale from single-celled organisms such as desmids (from 10 micrometres across) and picozoa (less than 3 micrometres across), to the largest trees ( megaflora) such as the conifer Sequoia sempervirens (up to 380 feet (120 m) tall ) and the angiosperm Eucalyptus regnans (up to 325 feet (99 m) tall ).

The naming of plants is governed by the International Code of Nomenclature for algae, fungi, and plants and the International Code of Nomenclature for Cultivated Plants.

Evolutionary history

The ancestors of land plants evolved in water. An algal scum formed on the land 1,200 million years ago, but it was not until the Ordovician, around 450 million years ago, that the first land plants appeared, with a level of organisation like that of bryophytes. However, evidence from carbon isotope ratios in Precambrian rocks suggests that complex plants developed over 1000 mya.

Primitive land plants began to diversify in the late Silurian, around 420 million years ago. Bryophytes, club mosses, and ferns then appear in the fossil record. Early plant anatomy is preserved in cellular detail in an early Devonian fossil assemblage from the Rhynie chert. These early plants were preserved by being petrified in chert formed in silica-rich volcanic hot springs.

By the end of the Devonian, most of the basic features of plants today were present, including roots, leaves and secondary wood in trees such as Archaeopteris. The Carboniferous Period saw the development of forests in swampy environments dominated by clubmosses and horsetails, including some as large as trees, and the appearance of early gymnosperms, the first seed plants. The Permo-Triassic extinction event radically changed the structures of communities. This may have set the scene for the evolution of flowering plants in the Triassic (~ 200 million years ago), with an adaptive radiation in the Cretaceous so rapid that Darwin called it an " abominable mystery". Conifers diversified from the Late Triassic onwards, and became a dominant part of floras in the Jurassic.

In 2019, a phylogeny based on genomes and transcriptomes from 1,153 plant species was proposed. The placing of algal groups is supported by phylogenies based on genomes from the Mesostigmatophyceae and Chlorokybophyceae that have since been sequenced. Both the "chlorophyte algae" and the "streptophyte algae" are treated as paraphyletic (vertical bars beside phylogenetic tree diagram) in this analysis, as the land plants arose from within those groups. The classification of Bryophyta is supported both by Puttick et al. 2018, and by phylogenies involving the hornwort genomes that have also since been sequenced.

Physiology

Plant cells

Plant cell structure

Plant cells have distinctive features that other eukaryotic cells (such as those of animals) lack. These include the large water-filled central vacuole, chloroplasts, and the strong flexible cell wall, which is outside the cell membrane. Chloroplasts are derived from what was once a symbiosis of a non-photosynthetic cell and photosynthetic cyanobacteria. The cell wall, made mostly of cellulose, allows plant cells to swell up with water without bursting. The vacuole allows the cell to change in size while the amount of cytoplasm stays the same.

Plant structure

Anatomy of a seed plant. 1. Shoot system. 2. Root system. 3. Hypocotyl. 4. Terminal bud. 5. Leaf blade. 6. Internode. 7. Axillary bud. 8. Petiole. 9. Stem. 10. Node. 11. Tap root. 12. Root hairs. 13. Root tip. 14. Root cap

Most plants are multicellular. Plant cells differentiate into multiple cell types, forming tissues such as the vascular tissue with specialized xylem and phloem of leaf veins and stems, and organs with different physiological functions such as roots to absorb water and minerals, stems for support and to transport water and synthesized molecules, leaves for photosynthesis, and flowers for reproduction.

Photosynthesis

Plants photosynthesize, manufacturing food molecules ( sugars) using energy obtained from light. Plant cells contain chlorophylls inside their chloroplasts, which are green pigments that are used to capture light energy. The end-to-end chemical equation for photosynthesis is:

This causes plants to release oxygen into the atmosphere. Green plants provide a substantial proportion of the world's molecular oxygen, alongside the contributions from photosynthetic algae and cyanobacteria.

Plants that have secondarily adopted a parasitic lifestyle may lose the genes involved in photosynthesis and the production of chlorophyll.

Growth and repair

Growth is determined by the interaction of a plant's genome with its physical and biotic environment. Factors of the physical or abiotic environment include temperature, water, light, carbon dioxide, and nutrients in the soil. Biotic factors that affect plant growth include crowding, grazing, beneficial symbiotic bacteria and fungi, and attacks by insects or plant diseases.

Frost and dehydration can damage or kill plants. Some plants have antifreeze proteins, heat-shock proteins and sugars in their cytoplasm that enable them to tolerate these stresses. Plants are continuously exposed to a range of physical and biotic stresses which cause DNA damage, but they can tolerate and repair much of this damage.

Reproduction

Plants reproduce to generate offspring, whether sexually, involving gametes, or asexually, involving ordinary growth. Many plants use both mechanisms.

Alternation of generations between a haploid (n) gametophyte (top) and a diploid (2n) sporophyte (bottom), in all types of plant

When reproducing sexually, plants have complex lifecycles involving alternation of generations. One generation, the sporophyte, which is diploid (with 2 sets of chromosomes), gives rise to the next generation, the gametophyte, which is haploid (with one set of chromosomes). Some plants also reproduce asexually via spores. In some non-flowering plants such as mosses, the sexual gametophyte forms most of the visible plant. In seed plants (gymnosperms and flowering plants), the sporophyte forms most of the visible plant, and the gametophyte is very small. Flowering plants reproduce sexually using flowers, which contain male and female parts: these may be within the same ( hermaphrodite) flower, on different flowers on the same plant, or on different plants. The pollen produces male gametes that enter the ovule to fertilize the egg cell of the female gametophyte. Fertilization takes place within the carpels or ovaries, which develop into fruits that contain seeds. Fruits may be dispersed whole, or they may split open and the seeds dispersed individually.

Ficinia spiralis spreads asexually with runners in the sand.

Plants reproduce asexually by growing any of a wide variety of structures capable of growing into new plants. At the simplest, plants such as mosses or liverworts may be broken into pieces, each of which may regrow into whole plants. The propagation of flowering plants by cuttings is a similar process. Structures such as runners enable plants to grow to cover an area, forming a clone. Many plants grow food storage structures such as tubers or bulbs which may each develop into a new plant.

Some non-flowering plants, such as many liverworts, mosses and some clubmosses, along with a few flowering plants, grow small clumps of cells called gemmae which can detach and grow.

Disease resistance

Plants use pattern-recognition receptors to recognize pathogens such as bacteria that cause plant diseases. This recognition triggers a protective response. The first such plant receptors were identified in rice and in Arabidopsis thaliana.

Plants have some of the largest genomes among all organisms. The largest plant genome (in terms of gene number) is that of wheat ( Triticum aestivum), predicted to encode ≈94,000 genes and thus almost 5 times as many as the human genome. The first plant genome sequenced was that of Arabidopsis thaliana which encodes about 25,500 genes. In terms of sheer DNA sequence, the smallest published genome is that of the carnivorous bladderwort ( Utricularia gibba) at 82 Mb (although it still encodes 28,500 genes) while the largest, from the Norway spruce ( Picea abies), extends over 19.6 Gb (encoding about 28,300 genes).

Distribution

A map of a classification of the world's vegetation into biomes. Those named here include tundra, taiga, temperate broadleaf forest, temperate steppe, subtropical rainforest, Mediterranean vegetation, monsoon forest, arid desert, xeric shrubland, dry steppe, semiarid desert, grass savanna, tree savanna, subtropical and tropical dry forest, tropical rainforest, alpine tundra, and montane forests. Shown in gray is "ice sheet and polar desert" devoid of plants.

Plants are distributed almost worldwide. While they inhabit several biomes which can be divided into a multitude of ecoregions, only the hardy plants of the Antarctic flora, consisting of algae, mosses, liverworts, lichens, and just two flowering plants, have adapted to the prevailing conditions on that southern continent.

Plants are often the dominant physical and structural component of the habitats where they occur. Many of the Earth's biomes are named for the type of vegetation because plants are the dominant organisms in those biomes, such as grassland, savanna, and tropical rainforest.

Primary producers

The photosynthesis conducted by land plants and algae is the ultimate source of energy and organic material in nearly all ecosystems. Photosynthesis, at first by cyanobacteria and later by photosynthetic eukaryotes, radically changed the composition of the early Earth's anoxic atmosphere, which as a result is now 21% oxygen. Animals and most other organisms are aerobic, relying on oxygen; those that do not are confined to relatively rare anaerobic environments. Plants are the primary producers in most terrestrial ecosystems and form the basis of the food web in those ecosystems. Plants form about 80% of the world biomass at about 450 gigatonnes (4.4×10 ¹¹ long tons; 5.0×10 ¹¹ short tons) of carbon.

Ecological relationships

Numerous animals have coevolved with plants; flowering plants have evolved pollination syndromes, suites of flower traits that favour their reproduction. Many, including insect and bird partners, are pollinators, visiting flowers and accidentally transferring pollen in exchange for food in the form of pollen or nectar.

Many animals disperse seeds that are adapted for such dispersal. Various mechanisms of dispersal have evolved. Some fruits offer nutritious outer layers attractive to animals, while the seeds are adapted to survive the passage through the animal's gut; others have hooks that enable them to attach to a mammal's fur. Myrmecophytes are plants that have coevolved with ants. The plant provides a home, and sometimes food, for the ants. In exchange, the ants defend the plant from herbivores and sometimes competing plants. Ant wastes serve as organic fertilizer.

The majority of plant species have fungi associated with their root systems in a mutualistic symbiosis known as mycorrhiza. The fungi help the plants gain water and mineral nutrients from the soil, while the plant gives the fungi carbohydrates manufactured in photosynthesis. Some plants serve as homes for endophytic fungi that protect the plant from herbivores by producing toxins. The fungal endophyte Neotyphodium coenophialum in tall fescue grass has pest status in the American cattle industry.

Many legumes have nitrogen-fixing bacteria in nodules of their roots, which fix nitrogen from the air for the plant to use; in return, the plants supply sugars to the bacteria. Nitrogen fixed in this way can become available to other plants, and is important in agriculture; for example, farmers may grow a crop rotation of a legume such as beans, followed by a cereal such as wheat, to provide cash crops with a reduced input of nitrogen fertilizer.

Some 1% of plants are parasitic. They range from the semi-parasitic mistletoe that merely takes some nutrients from its host, but still has photosynthetic leaves, to the fully-parasitic broomrape and toothwort that acquire all their nutrients through connections to the roots of other plants, and so have no chlorophyll. Full parasites can be extremely harmful to their plant hosts.

Plants that grow on other plants, usually trees, without parasitizing them, are called epiphytes. These may support diverse arboreal ecosystems. Some may indirectly harm their host plant, such as by intercepting light. Hemiepiphytes like the strangler fig begin as epiphytes, but eventually set their own roots and overpower and kill their host. Many orchids, bromeliads, ferns, and mosses grow as epiphytes. Among the epiphytes, the bromeliads accumulate water in their leaf axils; these water-filled cavities can support complex aquatic food webs.

Some 630 species of plants are carnivorous, such as the Venus flytrap ( Dionaea muscipula) and sundew ( Drosera species). They trap small animals and digest them to obtain mineral nutrients, especially nitrogen and phosphorus.

Competition

Competition for shared resources reduces a plant's growth. Shared resources include sunlight, water and nutrients. Light is a critical resource because it is necessary for photosynthesis. Plants use their leaves to shade other plants from sunlight and grow quickly to maximize their own expose. Water too is essential for photosynthesis; roots compete to maximize water uptake from soil. Some plants have deep roots that are able to locate water stored deep underground, and others have shallower roots that are capable of extending longer distances to collect recent rainwater. Minerals are important for plant growth and development. Common nutrients competed for amongst plants include nitrogen, phosphorus, and potassium.

Importance to humans

Human cultivation of plants is the core of agriculture, which in turn has played a key role in the history of world civilizations. Humans depend on plants for food, either directly or as feed in animal husbandry. Agriculture includes agronomy for arable crops, horticulture for vegetables and fruit, and forestry for timber. About 7,000 species of plant have been used for food, though most of today's food is derived from only 30 species. The major staples include cereals such as rice and wheat, starchy roots and tubers such as cassava and potato, and legumes such as peas and beans. Vegetable oils such as olive oil and palm oil provide lipids, while fruit and vegetables contribute vitamins and minerals to the diet. Coffee, tea, and chocolate are major crops whose caffeine-containing products serve as mild stimulants. The study of plant uses by people is called economic botany or ethnobotany.

Medicinal plants are a primary source of organic compounds, both for their medicinal and physiological effects, and for the industrial synthesis of a vast array of organic chemicals. Many hundreds of medicines, as well as narcotics, are derived from plants, both traditional medicines used in herbalism and chemical substances purified from plants or first identified in them, sometimes by ethnobotanical search, and then synthesised for use in modern medicine. Modern medicines derived from plants include aspirin, taxol, morphine, quinine, reserpine, colchicine, digitalis and vincristine. Plants used in herbalism include ginkgo, echinacea, feverfew, and Saint John's wort. The pharmacopoeia of Dioscorides, De materia medica, describing some 600 medicinal plants, was written between 50 and 70 CE and remained in use in Europe and the Middle East until around 1600 CE; it was the precursor of all modern pharmacopoeias.

Nonfood products

Plants grown as industrial crops are the source of a wide range of products used in manufacturing. Nonfood products include essential oils, natural dyes, pigments, waxes, resins, tannins, alkaloids, amber and cork. Products derived from plants include soaps, shampoos, perfumes, cosmetics, paint, varnish, turpentine, rubber, latex, lubricants, linoleum, plastics, inks, and gums. Renewable fuels from plants include firewood, peat and other biofuels. The fossil fuels coal, petroleum and natural gas are derived from the remains of aquatic organisms including phytoplankton in geological time. Many of the coal fields date to the Carboniferous period of Earth's history. Terrestrial plants also form type III kerogen, a source of natural gas.

Structural resources and fibres from plants are used to construct dwellings and to manufacture clothing. Wood is used for buildings, boats, and furniture, and for smaller items such as musical instruments and sports equipment. Wood is pulped to make paper and cardboard. Cloth is often made from cotton, flax, ramie or synthetic fibres such as rayon, derived from plant cellulose. Thread used to sew cloth likewise comes in large part from cotton.

Ornamental plants

A rose espalier at Niedernhall in Germany

Thousands of plant species are cultivated for their beauty and to provide shade, modify temperatures, reduce wind, abate noise, provide privacy, and reduce soil erosion. Plants are the basis of a multibillion-dollar per year tourism industry, which includes travel to historic gardens, national parks, rainforests, forests with colourful autumn leaves, and festivals such as Japan's and America's cherry blossom festivals.

Plants may be grown indoors as houseplants, or in specialized buildings such as greenhouses. Plants such as Venus flytrap, sensitive plant and resurrection plant are sold as novelties. Art forms specializing in the arrangement of cut or living plant include bonsai, ikebana, and the arrangement of cut or dried flowers. Ornamental plants have sometimes changed the course of history, as in tulipomania.

The traditional study of plants is the science of botany. Basic biological research has often used plants as its model organisms. In genetics, the breeding of pea plants allowed Gregor Mendel to derive the basic laws governing inheritance, and examination of chromosomes in maize allowed Barbara McClintock to demonstrate their connection to inherited traits. The plant Arabidopsis thaliana is used in laboratories as a model organism to understand how genes control the growth and development of plant structures. Tree rings provide a method of dating in archeology, and a record of past climates. The study of plant fossils, or Paleobotany, provides information about the evolutions of plants, paleogeographical reconstructions, and past climate change. Plant fossils can also help determine the age of rocks.

In mythology, religion, and culture

Plants including trees appear in mythology, religion, and literature. In multiple Indo-European, Siberian, and Native American religions, the world tree motif is depicted as a colossal tree growing on the earth, supporting the heavens, and with its roots reaching into the underworld. It may also appear as a cosmic tree or an eagle and serpent tree. Forms of the world tree include the archetypal tree of life, which is in turn connected to the Eurasian concept of the sacred tree. Another widespread ancient motif, found for example in Iran, has a tree of life flanked by a pair of confronted animals.

Flowers are often used as memorials, gifts and to mark special occasions such as births, deaths, weddings and holidays. Flower arrangements may be used to send hidden messages. Plants and especially flowers form the subjects of many paintings.

Negative effects

The musk thistle is an invasive species in Texas.

Weeds are commercially or aesthetically undesirable plants growing in managed environments such as in agriculture and gardens. People have spread many plants beyond their native ranges; some of these plants have become invasive, damaging existing ecosystems by displacing native species, and sometimes becoming serious weeds of cultivation.

Some plants that produce windblown pollen, including grasses, invoke allergic reactions in people who suffer from hay fever. Many plants produce toxins to protect themselves from herbivores. Major classes of plant toxins include alkaloids, terpenoids, and phenolics. These can be harmful to humans and livestock by ingestion or, as with poison ivy, by contact. Some plants have negative effects on other plants, preventing seedling growth or the growth of nearby plants by releasing allopathic chemicals.

References

Further reading

General:

Evans, L.T. (1998). Feeding the Ten Billion - Plants and Population Growth. Cambridge University Press. Paperback, 247 pages. ISBN 0-521-64685-5.

Kenrick, Paul & Crane, Peter R. (1997). The Origin and Early Diversification of Land Plants: A Cladistic Study. Washington, D.C.: Smithsonian Institution Press. ISBN 1-56098-730-8.

Raven, Peter H.; Evert, Ray F.; & Eichhorn, Susan E. (2005). Biology of Plants (7th ed.). New York: W.H. Freeman and Company. ISBN 0-7167-1007-2.

Taylor, Thomas N. & Taylor, Edith L. (1993). The Biology and Evolution of Fossil Plants. Englewood Cliffs, NJ: Prentice Hall. ISBN 0-13-651589-4.

Species estimates and counts:

External links

Botanical and vegetation databases

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Plants Scientific classification Domain: Eukaryota Clade: Diaphoretickes (unranked): Archaeplastida Kingdom: Plantae H.F.Copel., 1956 Superdivisions see text Synonyms Viridiplantae Cavalier-Smith 1981 [1] Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004 [2] Chlorobiota Kenrick and Crane 1997 [3] Chloroplastida Adl et al., 2005 [4] Phyta Barkley 1939 emend.

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A fungi is any member of the group of eukaryotic organisms that includes microorganisms such as yeast and molds, as well as the more familiar mushrooms.

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A fungus (: 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 , 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.

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 ('sponge') and ('mold').

The word 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 (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 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

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:

Shared features:

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.

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.

Bracket fungi on a tree stump

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.

Widespread white fungus in wood chip mulch in an Oklahoma garden[48]

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.

In 1729, Pier Antonio Micheli first published descriptions of fungi.

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.

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

An environmental isolate of Penicillium

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, 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 9,000years.

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

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. The pressure generated by the appressorium, directed against the plant epidermis, can exceed 8 megapascals (1,200 psi). 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.

The fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixed by other organisms for metabolism. Fungi have evolved a high degree of metabolic versatility that allows them to use a diverse range of organic substrates for growth, including simple compounds such as nitrate, ammonia, acetate, or ethanol. In some species the pigment melanin may play a role in extracting energy from ionizing radiation, such as gamma radiation. This form of "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlying biophysical and biochemical processes are not well known. This process might bear similarity to CO₂ fixation via visible light, but instead uses ionizing radiation as a source of energy.

Reproduction

Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms. It is estimated that a third of all fungi reproduce using more than one method of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph (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

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).

The 8-spore asci of Morchella elata, viewed with phase contrast microscopy

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 0.01-0.02cm, 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.

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.

Prototaxites milwaukeensis (Penhallow, 1908)-a Middle Devonian fungus from Wisconsin

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 760-1060Ma on the basis of comparisons of the rate of evolution in closely related groups. For much of the Paleozoic Era (542-251Ma), 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 (542-488.3Ma), also long before land plants. Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460Ma) 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 (416-359.2Ma), when they occur abundantly in the Rhynie chert, mostly as Zygomycota and Chytridiomycota. At about this same time, approximately 400Ma, the Ascomycota and Basidiomycota diverged, and all modern classes of fungi were present by the Late Carboniferous ( Pennsylvanian, 318.1-299Ma).

Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 415Ma; 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, 90Ma.

Some time after the Permian-Triassic extinction event (251.4Ma), 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".

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.

Taxonomic groups

Main groups of fungi

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, Zoopagomycota, 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.

Arbuscular mycorrhiza seen under microscope. Flax root cortical cells containing paired arbuscules.

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 species, capable of ejecting spores several meters through the air. Medically relevant genera include , Rhizomucor, and .

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, , and ), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes include Aspergillus, Penicillium, , and . 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, 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" , 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.

A pin mold decomposing a peach

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.

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.

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

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 ) 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 , 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 and 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.

As pathogens and parasites

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 , , 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, , 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

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

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 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 . 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 , which is a conserved homologue of genes in bacteria and 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.

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

The mold Penicillium rubens was the source of penicillin G.[241]

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 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

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 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.

A selection of edible mushrooms eaten in Asia

Edible mushrooms include commercially raised and wild-harvested fungi. Agaricus bisporus, sold as button mushrooms when small or Portobello mushrooms when larger, is the most widely cultivated species in the West, used in salads, soups, and many other dishes. Many Asian fungi are commercially grown and have increased in popularity in the West. They are often available fresh in grocery stores and markets, including straw mushrooms (Volvariella volvacea), oyster mushrooms (Pleurotus ostreatus), shiitakes (Lentinula edodes), and enokitake (Flammulina spp.).

Stilton cheese veined with Penicillium roqueforti

Many other mushroom species are harvested from the wild for personal consumption or commercial sale. Milk mushrooms, morels, chanterelles, truffles, black trumpets, and porcini mushrooms (Boletus edulis) (also known as king boletes) demand a high price on the market. They are often used in gourmet dishes.

Certain types of cheeses require inoculation of milk curds with fungal species that impart a unique flavor and texture to the cheese. Examples include the blue color in cheeses such as Stilton or Roquefort, which are made by inoculation with Penicillium roqueforti. Molds used in cheese production are non-toxic and are thus safe for human consumption; however, mycotoxins (e.g., aflatoxins, roquefortine C, patulin, or others) may accumulate because of growth of other fungi during cheese ripening or storage.

Poisonous fungi

Amanita phalloides accounts for the majority of fatal mushroom poisonings worldwide. It sometimes lacks the greenish color seen here.

Many mushroom species are poisonous to humans and cause a range of reactions including slight digestive problems, allergic reactions, hallucinations, severe organ failure, and death. Genera with mushrooms containing deadly toxins include , , and the most infamous, . The latter genus includes the destroying angel 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 it was implicated in serious poisonings causing rhabdomyolysis. Fly agaric mushrooms ( Amanita muscaria) also cause occasional non-fatal poisonings, mostly as a result of ingestion 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 northeastern 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

In 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 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 spp., Hirsutella spp., Paecilomyces ( Isaria) spp., and Lecanicillium lecanii. Endophytic fungi of grasses of the genus , such as E. coenophiala, 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 Epichloë 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.

Bioremediation

Certain fungi, in particular white-rot fungi, can degrade insecticides, herbicides, pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, water, and basic elements. Fungi have been shown to biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.

Model organisms

Several pivotal discoveries in biology were made by researchers using fungi as model organisms, that is, fungi that grow and sexually reproduce rapidly in the laboratory. For example, the one gene-one enzyme hypothesis was formulated by scientists using the bread mold Neurospora crassa to test their biochemical theories. Other important model fungi are Aspergillus nidulans and the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, each of which with a long history of use to investigate issues in eukaryotic cell biology and genetics, such as cell cycle regulation, chromatin structure, and gene regulation. Other fungal models have emerged that address specific biological questions relevant to medicine, plant pathology, and industrial uses; examples include Candida albicans, a dimorphic, opportunistic human pathogen, Magnaporthe grisea, a plant pathogen, and Pichia pastoris, a yeast widely used for eukaryotic protein production.

Fungi are used extensively to produce industrial chemicals like citric, gluconic, lactic, and malic acids, and industrial enzymes, such as lipases used in biological detergents, cellulases used in making cellulosic ethanol and stonewashed jeans, and amylases, invertases, proteases and xylanases.

References

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A fungus (: 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.

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Monerans are members of the kingdom Monera, which includes organisms more often called prokaryotes; the two terms are interchangeable.

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Monera (/məˈnɪərə/) (Greek - μονήρης (monḗrēs), "single", "solitary") is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus.

The taxon Monera was first proposed as a phylum by Ernst Haeckel in 1866. Subsequently, the phylum was elevated to the rank of kingdom in 1925 by Édouard Chatton. The last commonly accepted mega-classification with the taxon Monera was the five-kingdom classification system was established by Robert Whittaker in 1969.

Under the three-domain system of taxonomy, introduced by Carl Woese in 1977, which reflects the evolutionary history of life, the organisms found in kingdom Monera have been divided into two domains, Archaea and Bacteria (with Eukarya as the third domain). Furthermore, the taxon Monera is paraphyletic (does not include all descendants of their most recent common ancestor), as Archaea and Eukarya are currently believed to be more closely related than either is to Bacteria. The term "moneran" is the informal name of members of this group and is still sometimes used (as is the term "prokaryote") to denote a member of either domain.

Most bacteria were classified under Monera; however, some Cyanobacteria (often called the blue-green algae) were initially classified under Plantae due to their ability to photosynthesize.

Haeckel's classification

Traditionally the natural world was classified as animal, vegetable, or mineral as in Systema Naturae. After the development of the microscope, attempts were made to fit microscopic organisms into either the plant or animal kingdoms. In 1675, Antonie van Leeuwenhoek discovered bacteria and called them "animalcules", assigning them to the class Vermes of the Animalia. Due to the limited tools - the sole references for this group were shape, behaviour, and habitat - the description of genera and their classification was extremely limited, which was accentuated by the perceived lack of importance of the group.

Ten years after The Origin of Species by Charles Darwin, in 1866 Ernst Haeckel, a supporter of evolutionary theory, proposed a three-kingdom system that added the Protista as a new kingdom that contained most microscopic organisms. One of his eight major divisions of Protista was composed of the monerans (called Moneres by Haeckel), which he defined as completely structure-less and homogeneous organisms, consisting only of a piece of plasma. Haeckel's Monera included not only bacterial groups of early discovery but also several small eukaryotic organisms; in fact the genus Vibrio is the only bacterial genus explicitly assigned to the phylum, while others are mentioned indirectly, which led Copeland to speculate that Haeckel considered all bacteria to belong to the genus Vibrio, ignoring other bacterial genera. One notable exception were the members of the modern phylum Cyanobacteria, such as , which were placed in the phylum Archephyta of Algae (vide infra: Blue-green algae).

The Neolatin noun Monera and the German noun Moneren/Moneres are derived from the ancient Greek noun moneres, which Haeckel stated meant "simple"; however, it actually means "single, solitary". Haeckel also describes the protist genus Monas in the two pages about Monera in his 1866 book. The informal name of a member of the Monera was initially moneron, but later moneran was used.

Due to its lack of features, the phylum was not fully subdivided, but the genera therein were divided into two groups:

die Gymnomoneren (no envelope [sic.]): Gymnomonera

Protogenes - such as Protogenes primordialis, an unidentified amoeba (eukaryote) and not a bacterium

Protamaeba- an incorrectly described/fabricated species

- a genus of comma-shaped bacteria first described in 1854

Bacterium - a genus of rod-shaped bacteria first described in 1828. Haeckel does not explicitly assign this genus to the Monera.

- a genus of spore-forming rod-shaped bacteria first described in 1835 Haeckel does not explicitly assign this genus to the Monera kingdom.

Spirochaeta - thin spiral-shaped bacteria first described in 1835 Haeckel does not explicitly assign this genus to the Monera.

- spiral-shaped bacteria first described in 1832 Haeckel does not explicitly assign this genus to the Monera.

etc.: Haeckel does provide a comprehensive list.

die Lepomoneren (with envelope): Lepomonera

Protomonas - identified to a synonym of , a flagellated protozoan, and not a bacterium. The name was reused in 1984 for an unrelated genus of bacteria.

Vampyrella - now classed as a eukaryote and not a bacterium.

Subsequent classifications

Like Protista, the Monera classification was not fully followed at first and several different ranks were used and located with animals, plants, protists or fungi. Furthermore, Haeckel's classification lacked specificity and was not exhaustive - it in fact covers only a few pages-, consequently a lot of confusion arose even to the point that the Monera did not contain bacterial genera and others according to Huxley. They were first recognized as a kingdom by Enderlein in 1925 (Bakterien-Cyclogenie. de Gruyter, Berlin).

The most popular scheme was created in 1859 by C. Von Nägeli who classified non-phototrophic Bacteria as the class Schizomycetes.

The class Schizomycetes was then emended by Walter Migula (along with the coinage of the genus Pseudomonas in 1894) and others. This term was in dominant use even in 1916 as reported by Robert Earle Buchanan, as it had priority over other terms such as Monera. However, starting with Ferdinand Cohn in 1872 the term bacteria (or in German ) became prominently used to informally describe this group of species without a nucleus: Bacterium was in fact a genus created in 1828 by Christian Gottfried Ehrenberg Additionally, Cohn divided the bacteria according to shape namely:

Spherobacteria for the cocci

Microbacteria for the short, non-filamentous rods

Desmobacteria for the longer, filamentous rods and Spirobacteria for the spiral forms.

Successively, Cohn created the Schizophyta of Plants, which contained the non-photrophic bacteria in the family Schizomycetes and the phototrophic bacteria (blue green algae/Cyanobacteria) in the Schizophyceae This union of blue green algae and Bacteria was much later followed by Haeckel, who classified the two families in a revised phylum Monera in the Protista.

Stanier and van Neil (1941, The main outlines of bacterial classification. J Bacteriol 42: 437- 466) recognized the Kingdom Monera with two phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae (3 orders), Myxobacteriae (1 order), and Spirochetae (1 order); Bisset (1962, Bacteria, 2nd ed., Livingston, London) distinguished 1 class and 4 orders: Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales; Orla-Jensen (1909, Die Hauptlinien des naturalischen Bakteriensystems nebst einer Ubersicht der Garungsphenomene. Zentr. Bakt. Parasitenk., II, 22: 305-346) and Bergey et al (1925, Bergey's Manual of Determinative Bacteriology, Baltimore : Williams & Wilkins Co.) with many subsequent editions) also presented classifications.

Rise to prominence

The term Monera became well established in the 20s and 30s when to rightfully increase the importance of the difference between species with a nucleus and without. In 1925, Édouard Chatton divided all living organisms into two empires Prokaryotes and Eukaryotes: the Kingdom Monera being the sole member of the Prokaryotes empire.[clarification needed ]

The anthropic importance of the crown group of animals, plants and fungi was hard to depose; consequently, several other megaclassification schemes ignored on the empire rank but maintained the kingdom Monera consisting of bacteria, such Copeland in 1938 and Whittaker in 1969. The latter classification system was widely followed, in which Robert Whittaker proposed a five kingdom system for classification of living organisms. Whittaker's system placed most single celled organisms into either the prokaryotic Monera or the eukaryotic Protista. The other three kingdoms in his system were the eukaryotic Fungi, Animalia, and Plantae. Whittaker, however, did not believe that all his kingdoms were monophyletic. Whittaker subdivided the kingdom into two branches containing several phyla:

Myxomonera branch

Mastigomonera branch

Alternative commonly followed subdivision systems were based on Gram stains. This culminated in the Gibbons and Murray classification of 1978:

Gracilicutes (gram negative)

Photobacteria (photosynthetic): class Oxyphotobacteriae (water as electron acceptor, includes the order Cyanobacteriales = blue green algae, now phylum Cyanobacteria) and class Anoxyphotobacteriae (anaerobic phototrophs, orders: Rhodospirillales and Chlorobiales

Scotobacteria (non-photosynthetic, now the Proteobacteria and other gram negative nonphotosynthetic phyla) eg. Pseudomonas aeruginosa, Salmonella enterica, E.coli.

Firmacutes [sic] (gram positive, subsequently corrected to Firmicutes)
several orders such as Bacillales and Actinomycetales (now in the phylum Actinobacteria) eg. Bacillus cerus, Streptococcus, Staphylococcus.

Mollicutes (gram variable, e.g. Mycoplasma)

Mendocutes (uneven gram stain, "methanogenic bacteria" now known as the Archaea)

Three-domain system

In 1977, a PNAS paper by Carl Woese and George Fox demonstrated that the archaea (initially called archaebacteria) are not significantly closer in relationship to the bacteria than they are to eukaryotes. The paper received front-page coverage in The New York Times, and great controversy initially. The conclusions have since become accepted, leading to replacement of the kingdom Monera with the two domains Bacteria and Archaea. A minority of scientists, including Thomas Cavalier-Smith, continue to reject the widely accepted division between these two groups. Cavalier-Smith has published classifications in which the archaebacteria are part of a subkingdom of the Kingdom Bacteria.

Although it was generally accepted that one could distinguish prokaryotes from eukaryotes on the basis of the presence of a nucleus, mitosis versus binary fission as a way of reproducing, size, and other traits, the monophyly of the kingdom Monera (or for that matter, whether classification should be according to phylogeny) was controversial for many decades. Although distinguishing between prokaryotes from eukaryotes as a fundamental distinction is often credited to a 1937 paper by Édouard Chatton (little noted until 1962), he did not emphasize this distinction more than other biologists of his era. Roger Stanier and C. B. van Niel believed that the bacteria (a term which at the time did not include blue-green algae) and the blue-green algae had a single origin, a conviction that culminated in Stanier writing in a letter in 1970, "I think it is now quite evident that the blue-green algae are not distinguishable from bacteria by any fundamental feature of their cellular organization". Other researchers, such as E. G. Pringsheim writing in 1949, suspected separate origins for bacteria and blue-green algae. In 1974, the influential Bergey's Manual published a new edition coining the term cyanobacteria to refer to what had been called blue-green algae, marking the acceptance of this group within the Monera.

Monerans are a group of organisms having prokaryotic structure. Archaea differ from Bacteria in having a different 16S srna. They also have a different cell wall structure.

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Monera (/məˈnɪərə/) (Greek - μονήρης (monḗrēs), "single", "solitary") is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus. The taxon Monera was first proposed as a phylum by Ernst Haeckel in 1866.

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A protist is any eukaryotic organism one with cells containing a nucleus that is not an animal, plant or a fungus The protists do not form a natural group, or clade since they exclude certain eukaryotes; but, like algae or invertebrates.

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The 5 Kingdoms in Classification | Evolution | Biology | FuseSchool