Schematic two-dimensional cross-sectional view of glycogen: A core protein of glycogenin is surrounded by branches of glucose units. The entire globular granule may contain around 30,000 glucose units.A view of the atomic structure of a single branched strand of glucose units in a glycogen molecule.Glycogen (black granules) in spermatozoa of a flatworm; transmission electron microscopy, scale: 0.3 μm
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. It is the main storage form of glucose in the human body.
Glycogen functions as one of three regularly used forms of energy reserves, creatine phosphate being for very short-term, glycogen being for short-term and the triglyceride stores in adipose tissue
(i.e., body fat) being for long-term storage. Protein, broken down into
amino acids, is seldom used as a main energy source except during
starvation and glycolytic crisis (see bioenergetic systems).
In humans, glycogen is made and stored primarily in the cells of the liver and skeletal muscle. In the liver, glycogen can make up 5–6% of the organ's fresh weight:
the liver of an adult, weighing 1.5 kg, can store roughly 100–120 grams
of glycogen. In skeletal muscle, glycogen is found in a low concentration (1–2% of the muscle mass): the skeletal muscle of an adult weighing 70 kg stores roughly 400 grams of glycogen. Small amounts of glycogen are also found in other tissues and cells, including the kidneys, red blood cells, white blood cells, and glial cells in the brain. The uterus also stores glycogen during pregnancy to nourish the embryo.
The amount of glycogen stored in the body mostly depends on oxidative type 1 fibres, physical training, basal metabolic rate, and eating habits. Different levels of resting muscle glycogen are reached by changing the
number of glycogen particles, rather than increasing the size of
existing particles though most glycogen particles at rest are smaller than their theoretical maximum.
Approximately 4 grams of glucose are present in the blood of humans at all times; in fasting individuals, blood glucose
is maintained constant at this level at the expense of glycogen stores,
primarily from the liver (glycogen in skeletal muscle is mainly used as
an immediate source of energy for that muscle rather than being used to
maintain physiological blood glucose levels). Glycogen stores in skeletal muscle serve as a form of energy storage for the muscle itself; however, the breakdown of muscle glycogen impedes muscle glucose uptake
from the blood, thereby increasing the amount of blood glucose
available for use in other tissues. Liver glycogen stores serve as a store of glucose for use throughout the body, particularly the central nervous system. The human brain consumes approximately 60% of blood glucose in fasted, sedentary individuals.
Glycogen is an analogue of starch, a glucose polymer that functions as energy storage in plants. It has a structure similar to amylopectin (a component of starch), but is more extensively branched and compact than starch. Both are white powders in their dry state. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell types, and plays an important role in the glucose cycle. Glycogen forms an energy
reserve that can be quickly mobilized to meet a sudden need for
glucose, but one that is less compact than the energy reserves of triglycerides (lipids). As such it is also found as storage reserve in many parasitic protozoa.
Structure
α(1→4)-glycosidic linkages in the glycogen oligomerα(1→4)-glycosidic and α(1→6)-glycosidic linkages in the glycogen oligomer
Glycogen is a branched biopolymer consisting of linear chains of glucoseresidues with an average chain length of approximately 8–12 glucose units and 2,000-60,000 residues per one molecule of glycogen.
Like amylopectin, glucose units are linked together linearly by α(1→4) glycosidic bonds
from one glucose to the next. Branches are linked to the chains from
which they are branching off by α(1→6) glycosidic bonds between the
first glucose of the new branch and a glucose on the stem chain.
Each glycogen is essentially a ball of glucose trees, with around 12 layers, centered on a glycogenin
protein, with three kinds of glucose chains: A, B, and C. There is only
one C-chain, attached to the glycogenin. This C-chain is formed by the
self-glucosylation of the glycogenin, forming a short primer chain. From
the C-chain grows out B-chains, and from B-chains branch out B- and
A-chains. The B-chains have on average 2 branch points, while the
A-chains are terminal, thus unbranched. On average, each chain has
length 12, tightly constrained to be between 11 and 15. All A-chains
reach the spherical surface of the glycogen.
Glycogen in muscle, liver, and fat cells is stored in a hydrated
form, composed of three or four parts of water per part of glycogen
associated with 0.45 millimoles (18 mg) of potassium per gram of glycogen.
Glucose is an osmotic molecule, and can have profound effects on
osmotic pressure in high concentrations possibly leading to cell damage
or death if stored in the cell without being modified. Glycogen is a non-osmotic molecule, so it can be used as a solution to
storing glucose in the cell without disrupting osmotic pressure.
Functions
Liver
As a meal containing carbohydrates or protein is eaten and digested, blood glucose levels rise, and the pancreas secretes insulin. Blood glucose from the portal vein enters liver cells (hepatocytes). Insulin acts on the hepatocytes to stimulate the action of several enzymes, including glycogen synthase. Glucose molecules are added to the chains of glycogen as long as both insulin and glucose remain plentiful. In this postprandial or "fed" state, the liver takes in more glucose from the blood than it releases.
After a meal has been digested and glucose levels begin to fall,
insulin secretion is reduced, and glycogen synthesis stops. When it is
needed for energy, glycogen is broken down and converted again to glucose. Glycogen phosphorylase
is the primary enzyme of glycogen breakdown. For the next 8–12 hours,
glucose derived from liver glycogen is the primary source of blood
glucose used by the rest of the body for fuel.
Glucagon,
another hormone produced by the pancreas, in many respects serves as a
countersignal to insulin. In response to insulin levels being below
normal (when blood levels of glucose begin to fall below the normal
range), glucagon is secreted in increasing amounts and stimulates both glycogenolysis (the breakdown of glycogen) and gluconeogenesis (the production of glucose from other sources).
Muscle
Metabolism of common monosaccharides
Muscle glycogen appears to function as a reserve of quickly available phosphorylated glucose, in the form of glucose-1-phosphate, for muscle cells. Glycogen contained within skeletal muscle cells are primarily in the form of β particles. Other cells that contain small amounts use it locally as well. As muscle cells lack glucose-6-phosphatase,
which is required to pass glucose into the blood, the glycogen they
store is available solely for internal use and is not shared with other
cells. This is in contrast to liver cells, which, on demand, readily do
break down their stored glycogen into glucose and send it through the
blood stream as fuel for other organs.
Skeletal muscle needs ATP (provides energy) for muscle contraction and relaxation, in what is known as the sliding filament theory. Skeletal muscle relies predominantly on glycogenolysis
for the first few minutes as it transitions from rest to activity, as
well as throughout high-intensity aerobic activity and all anaerobic
activity. During anaerobic activity, such as weightlifting and isometric exercise, the phosphagen system (ATP-PCr) and muscle glycogen are the only substrates used as they do not require oxygen nor blood flow.
Different bioenergetic systems produce ATP at different speeds, with ATP produced from muscle glycogen being much faster than fatty acid oxidation. The level of exercise intensity
determines how much of which substrate (fuel) is used for ATP synthesis
also. Muscle glycogen can supply a much higher rate of substrate for
ATP synthesis than blood glucose. During maximum intensity exercise,
muscle glycogen can supply 40 mmol glucose/kg wet weight/minute, whereas blood glucose can supply 4 – 5 mmol.Due to its high supply rate and quick ATP synthesis, during
high-intensity aerobic activity (such as brisk walking, jogging, or
running), the higher the exercise intensity, the more the muscle cell
produces ATP from muscle glycogen. This reliance on muscle glycogen is not only to provide the muscle with
enough ATP during high-intensity exercise, but also to maintain blood
glucose homeostasis (that is, to not become hypoglycaemic by the muscles
needing to extract far more glucose from the blood than the liver can
provide). A deficit of muscle glycogen leads to muscle fatigue known as "hitting the wall" or "the bonk" (see below under glycogen depletion).
Structure type
In
1999, Meléndez et al claimed that the structure of glycogen is optimal
under a particular metabolic constraint model, where the structure was
suggested to be "fractal" in nature. However, research by Besford et al used small angle X-ray scattering experiments accompanied by branching
theory models to show that glycogen is a randomly hyperbranched polymer
nanoparticle. Glycogen is not fractal in nature. This has been
subsequently verified by others who have performed Monte Carlo simulations
of glycogen particle growth, and shown that the molecular density
reaches a maximum near the centre of the nanoparticle structure, not at
the periphery (contradicting a fractal structure that would have greater
density at the periphery).
History
Glycogen was discovered by Claude Bernard.
His experiments showed that the liver contained a substance that could
give rise to reducing sugar by the action of a "ferment" in the liver.
By 1857, he described the isolation of a substance he called "la matière glycogène",
or "sugar-forming substance". Soon after the discovery of glycogen in
the liver, M.A. Sanson found that muscular tissue also contains
glycogen. The empirical formula for glycogen of (C 6H 10O 5)n was established by August Kekulé in 1858.
Sanson, M. A. "Note sur la formation physiologique du sucre dans
l’economie animale." Comptes rendus des séances de l'Académie des
Sciences 44 (1857): 1323-5.
Glycogen synthesis is, unlike its breakdown, endergonic—it requires the input of energy. Energy for glycogen synthesis comes from uridine triphosphate (UTP), which reacts with glucose-1-phosphate, forming UDP-glucose, in a reaction catalysed by UTP—glucose-1-phosphate uridylyltransferase. Glycogen is synthesized from monomers of UDP-glucose initially by the protein glycogenin, which has two tyrosine
anchors for the reducing end of glycogen, since glycogenin is a
homodimer. After about eight glucose molecules have been added to a
tyrosine residue, the enzyme glycogen synthase
progressively lengthens the glycogen chain using UDP-glucose, adding
α(1→4)-bonded glucose to the nonreducing end of the glycogen chain.
The glycogen branching enzyme
catalyzes the transfer of a terminal fragment of six or seven glucose
residues from a nonreducing end to the C-6 hydroxyl group of a glucose
residue deeper into the interior of the glycogen molecule. The branching
enzyme can act upon only a branch having at least 11 residues, and the
enzyme may transfer to the same glucose chain or adjacent glucose
chains.
Glycogen is cleaved from the nonreducing ends of the chain by the enzyme glycogen phosphorylase to produce monomers of glucose-1-phosphate:
In vivo, phosphorolysis proceeds in the direction of glycogen
breakdown because the ratio of phosphate and glucose-1-phosphate is
usually greater than 100. Glucose-1-phosphate is then converted to glucose 6 phosphate (G6P) by phosphoglucomutase. A special debranching enzyme
is needed to remove the α(1→6) branches in branched glycogen and
reshape the chain into a linear polymer. The G6P monomers produced have
three possible fates:
G6P can continue on the glycolysis pathway and be used as fuel.
In the liver and kidney, G6P can be dephosphorylated back to glucose by the enzyme glucose 6-phosphatase. This is the final step in the gluconeogenesis pathway.
Clinical relevance
Disorders of glycogen metabolism
The most common disease in which glycogen metabolism becomes abnormal is diabetes,
in which, because of abnormal amounts of insulin, liver glycogen can be
abnormally accumulated or depleted. Restoration of normal glucose
metabolism usually normalizes glycogen metabolism, as well.
In hypoglycemia caused by excessive insulin, liver glycogen levels are high, but the high insulin levels prevent the glycogenolysis necessary to maintain normal blood sugar levels. Glucagon is a common treatment for this type of hypoglycemia.
Long-distance athletes, such as marathon runners, cross-country skiers, and cyclists,
often experience glycogen depletion, where almost all of the athlete's
glycogen stores are depleted after long periods of exertion without
sufficient carbohydrate consumption. This phenomenon is referred to as "hitting the wall" in running and "bonking" in cycling.
Glycogen depletion can be forestalled in three possible ways:
First, during exercise, carbohydrates with the highest possible rate of conversion to blood glucose (high glycemic index)
are ingested continuously. The best possible outcome of this strategy
replaces about 35% of glucose consumed at heart rates above about 80% of
maximum.
Second, through endurance training adaptations and specialized
regimens (e.g. fasting, low-intensity endurance training), the body can
condition type I muscle fibers to improve both fuel use efficiency and workload capacity to increase the percentage of fatty acids used as fuel,sparing carbohydrate use from all sources.
Third, by consuming large quantities of carbohydrates after
depleting glycogen stores as a result of exercise or diet, the body can
increase storage capacity of intramuscular glycogen stores. This process is known as carbohydrate loading.
In general, glycemic index of carbohydrate source does not matter since
muscular insulin sensitivity is increased as a result of temporary
glycogen depletion.
When athletes ingest both carbohydrate and caffeine following exhaustive exercise, their glycogen stores tend to be replenished more rapidly; however, the minimum dose of caffeine at which there is a clinically significant effect on glycogen repletion has not been established.
Quantum mechanics is the study of matter and matter's interactions with energy on the scale of atomic and subatomic particles. By contrast, classical physics
explains matter and energy only on a scale familiar to human
experience, including the behavior of astronomical bodies such as the
Moon. Classical physics is still used in much of modern science and
technology. However, towards the end of the 19th century, scientists
discovered phenomena in both the large (macro) and the small (micro) worlds that classical physics could not explain. The desire to resolve inconsistencies between observed phenomena and
classical theory led to a revolution in physics, a shift in the original
scientific paradigm: the development of quantum mechanics.
Many aspects of quantum mechanics yield unexpected results, defying expectations and deemed counterintuitive. These aspects can seem paradoxical as they map behaviors quite differently from those seen at larger scales. In the words of quantum physicist Richard Feynman, quantum mechanics deals with "nature as She is—absurd". Features of quantum mechanics often defy simple explanations in everyday language. One example of this is the uncertainty principle: precise measurements of position cannot be combined with precise measurements of velocity. Another example is entanglement: a measurement made on one particle (such as an electron that is measured to have spin
'up') will correlate with a measurement on a second particle (an
electron will be found to have spin 'down') if the two particles have a
shared history. This will apply even if it is impossible for the result
of the first measurement to have been transmitted to the second particle
before the second measurement takes place.
Quantum mechanics helps people understand chemistry, because it explains how atoms interact with each other and form molecules. Many remarkable phenomena can be explained using quantum mechanics, like superfluidity. For example, if liquid helium cooled to a temperature near absolute zero
is placed in a container, it spontaneously flows up and over the rim of
its container; this is an effect which cannot be explained by classical
physics.
James C. Maxwell's unification of the equations
governing electricity, magnetism, and light in the late 19th century
led to experiments on the interaction of light and matter. Some of these
experiments had aspects which could not be explained until quantum
mechanics emerged in the early part of the 20th century.
The seeds of the quantum revolution appear in the discovery by J.J. Thomson in 1897 that cathode rays were not continuous but "corpuscles" (electrons). Electrons had been named just six years earlier as part of the emerging theory of atoms. In 1900, Max Planck, unconvinced by the atomic theory, discovered that he needed discrete entities like atoms or electrons to explain black-body radiation.
Black-body radiation intensity vs color and temperature. The rainbow bar represents visible light; 5000 K
objects are "white hot" by mixing differing colors of visible light. To
the right is the invisible infrared. Classical theory (black curve for
5000 K) fails to predict the colors; the other curves are correctly
predicted by quantum theories.
Very hot – red hot or white hot – objects look similar when heated to
the same temperature. This look results from a common curve of light
intensity at different frequencies (colors), which is called black-body
radiation. White hot objects have intensity across many colors in the
visible range. The lowest frequencies above visible colors are infrared light,
which also give off heat. Continuous wave theories of light and matter
cannot explain the black-body radiation curve. Planck spread the heat
energy among individual "oscillators" of an undefined character but with
discrete energy capacity; this model explained black-body radiation.
At the time, electrons, atoms, and discrete oscillators were all exotic ideas to explain exotic phenomena. But in 1905 Albert Einstein
proposed that light was also corpuscular, consisting of "energy
quanta", in contradiction to the established science of light as a
continuous wave, stretching back a hundred years to Thomas Young's work on diffraction.
Einstein's revolutionary proposal started by reanalyzing Planck's
black-body theory, arriving at the same conclusions by using the new
"energy quanta". Einstein then showed how energy quanta connected to
Thomson's electron. In 1902, Philipp Lenard
directed light from an arc lamp onto freshly cleaned metal plates
housed in an evacuated glass tube. He measured the electric current
coming off the metal plate, at higher and lower intensities of light and
for different metals. Lenard showed that amount of current – the number
of electrons – depended on the intensity of the light, but that the
velocity of these electrons did not depend on intensity. This is the photoelectric effect.
The continuous wave theories of the time predicted that more light
intensity would accelerate the same amount of current to higher
velocity, contrary to this experiment. Einstein's energy quanta
explained the volume increase: one electron is ejected for each quantum:
more quanta mean more electrons.
Einstein then predicted that the electron velocity would increase
in direct proportion to the light frequency above a fixed value that
depended upon the metal. Here the idea is that energy in energy-quanta
depends upon the light frequency; the energy transferred to the electron
comes in proportion to the light frequency. The type of metal gives a barrier, the fixed value, that the electrons must climb over to exit their atoms, to be emitted from the metal surface and be measured.
Ten years elapsed before Millikan's definitive experiment verified Einstein's prediction. During that time many scientists rejected the revolutionary idea of quanta. But Planck's and Einstein's concept was in the air and soon began to affect other physics and quantum theories.
Experiments with light and matter in the late 1800s uncovered a
reproducible but puzzling regularity. When light was shown through
purified gases, certain frequencies (colors) did not pass. These dark
absorption 'lines' followed a distinctive pattern: the gaps between the
lines decreased steadily. By 1889, the Rydberg formula predicted the lines for hydrogen gas using only a constant number and the integers to index the lines. The origin of this regularity was unknown. Solving this mystery would
eventually become the first major step toward quantum mechanics.
Throughout the 19th century evidence grew for the atomic
nature of matter. With Thomson's discovery of the electron in 1897,
scientists began the search for a model of the interior of the atom.
Thomson proposed negative electrons swimming in a pool of positive charge. Between 1908 and 1911, Rutherford showed that the positive part was only 1/3000th of the diameter of the atom.
Models of "planetary" electrons orbiting a nuclear "Sun" were
proposed, but cannot explain why the electron does not simply fall into
the positive charge. In 1913 Niels Bohr and Ernest Rutherford
connected the new atom models to the mystery of the Rydberg formula:
the orbital radius of the electrons were constrained and the resulting
energy differences matched the energy differences in the absorption
lines. This meant that absorption and emission of light from atoms was
energy quantized: only specific energies that matched the difference in
orbital energy would be emitted or absorbed.
Trading one mystery – the regular pattern of the Rydberg formula –
for another mystery – constraints on electron orbits – might not seem
like a big advance, but the new atom model summarized many other
experimental findings. The quantization of the photoelectric effect and
now the quantization of the electron orbits set the stage for the final
revolution.
Throughout the first and the modern era of quantum mechanics the
concept that classical mechanics must be valid macroscopically
constrained possible quantum models. This concept was formalized by Bohr
in 1923 as the correspondence principle. It requires quantum theory to converge to classical limits.
A related concept is Ehrenfest's theorem, which shows that the average values obtained from quantum mechanics (e.g. position and momentum) obey classical laws.
Stern–Gerlach experiment:
Silver atoms travelling through an inhomogeneous magnetic field, and
being deflected up or down depending on their spin; (1) furnace, (2)
beam of silver atoms, (3) inhomogeneous magnetic field, (4) classically
expected result, (5) observed result
In 1922 Otto Stern and Walther Gerlachdemonstrated that the magnetic properties of silver atoms defy classical explanation, the work contributing to Stern’s 1943 Nobel Prize in Physics.
They fired a beam of silver atoms through a magnetic field. According
to classical physics, the atoms should have emerged in a spray, with a
continuous range of directions. Instead, the beam separated into two,
and only two, diverging streams of atoms. Unlike the other quantum effects known at the time, this striking result involves the state of a single atom.In 1927, Thomas Erwin Phipps and John Bellamy Taylor [de] obtained a similar, but less pronounced effect using hydrogen atoms in their ground state, thereby eliminating any doubts that may have been caused by the use of silver atoms.
In 1924, Wolfgang Pauli called it "two-valuedness not describable
classically" and associated it with electrons in the outermost shell. The experiments lead to formulation of its theory described to arise from spin of the electron in 1925, by Samuel Goudsmit and George Uhlenbeck, under the advice of Paul Ehrenfest.
In 1924 Louis de Broglie proposed that electrons in an atom are constrained not in "orbits" but as
standing waves. In detail his solution did not work, but his hypothesis –
that the electron "corpuscle" moves in the atom as a wave – spurred Erwin Schrödinger to develop a wave equation for electrons; when applied to hydrogen the Rydberg formula was accurately reproduced.
Example original electron diffraction photograph from the laboratory of G. P. Thomson, recorded 1925–1927
Max Born's 1924 paper "Zur Quantenmechanik" was the first use of the words "quantum mechanics" in print. His later work included developing quantum collision models; in a footnote to a 1926 paper he proposed the Born rule connecting theoretical models to experiment.
In 1927 at Bell Labs, Clinton Davisson and Lester Germerfired slow-moving electrons at a crystallinenickel target which showed a diffraction pattern indicating wave nature of electron whose theory was fully explained by Hans Bethe. A similar experiment by George Paget Thomson and Alexander Reid, firing electrons at thin celluloid foils and later metal films, observing rings, independently discovered matter wave nature of electrons.
Planck and Einstein started the revolution with quanta that broke
down the continuous models of matter and light. Twenty years later
"corpuscles" like electrons came to be modeled as continuous waves. This
result came to be called wave-particle duality, one iconic idea along
with the uncertainty principle that sets quantum mechanics apart from
older models of physics.
In 1923 Compton
demonstrated that the Planck-Einstein energy quanta from light also had
momentum; three years later the "energy quanta" got a new name "photon". Despite its role in almost all stages of the quantum revolution, no explicit model for light quanta existed until 1927 when Paul Dirac began work on a quantum theory of radiation that became quantum electrodynamics. Over the following decades this work evolved into quantum field theory, the basis for modern quantum optics and particle physics.
The concept of wave–particle duality says that neither the classical
concept of "particle" nor of "wave" can fully describe the behavior of
quantum-scale objects, either photons or matter. Wave–particle duality
is an example of the principle of complementarity in quantum physics. An elegant example of wave-particle duality is the double-slit experiment.
The
diffraction pattern produced when light is shone through one slit (top)
and the interference pattern produced by two slits (bottom). Both
patterns show oscillations due to the wave nature of light. The double
slit pattern is more dramatic.
In the double-slit experiment, as originally performed by Thomas Young in 1803, and then Augustin Fresnel a decade later, a beam of light is directed through two narrow, closely spaced slits, producing an interference pattern
of light and dark bands on a screen. The same behavior can be
demonstrated in water waves: the double-slit experiment was seen as a
demonstration of the wave nature of light.
Variations of the double-slit experiment have been performed using electrons, atoms, and even large molecules, and the same type of interference pattern is seen. Thus it has been demonstrated that all matter possesses wave characteristics.
If the source intensity is turned down, the same interference
pattern will slowly build up, one "count" or particle (e.g. photon or
electron) at a time. The quantum system acts as a wave when passing
through the double slits, but as a particle when it is detected. This is
a typical feature of quantum complementarity: a quantum system acts as a
wave in an experiment to measure its wave-like properties, and like a
particle in an experiment to measure its particle-like properties. The
point on the detector screen where any individual particle shows up is
the result of a random process. However, the distribution pattern of
many individual particles mimics the diffraction pattern produced by
waves.
Suppose it is desired to measure the position and speed of an
object—for example, a car going through a radar speed trap. It can be
assumed that the car has a definite position and speed at a particular
moment in time. How accurately these values can be measured depends on
the quality of the measuring equipment. If the precision of the
measuring equipment is improved, it provides a result closer to the true
value. It might be assumed that the speed of the car and its position
could be operationally defined and measured simultaneously, as precisely
as might be desired.
In 1927, Heisenberg proved that this last assumption is not correct. Quantum mechanics shows that certain pairs of physical properties, for
example, position and speed, cannot be simultaneously measured, nor
defined in operational terms, to arbitrary precision: the more precisely
one property is measured, or defined in operational terms, the less
precisely can the other be thus treated. This statement is known as the uncertainty principle.
The uncertainty principle is not only a statement about the accuracy of
our measuring equipment but, more deeply, is about the conceptual
nature of the measured quantities—the assumption that the car had
simultaneously defined position and speed does not work in quantum
mechanics. On a scale of cars and people, these uncertainties are
negligible, but when dealing with atoms and electrons they become
critical.
Heisenberg gave, as an illustration, the measurement of the position and momentum
of an electron using a photon of light. In measuring the electron's
position, the higher the frequency of the photon, the more accurate is
the measurement of the position of the impact of the photon with the
electron, but the greater is the disturbance of the electron. This is
because from the impact with the photon, the electron absorbs a random
amount of energy, rendering the measurement obtained of its momentum
increasingly uncertain, for one is necessarily measuring its post-impact
disturbed momentum from the collision products and not its original
momentum (momentum which should be simultaneously measured with
position). With a photon of lower frequency, the disturbance (and hence
uncertainty) in the momentum is less, but so is the accuracy of the
measurement of the position of the impact.
At the heart of the uncertainty principle is a fact that for any
mathematical analysis in the position and velocity domains, achieving a
sharper (more precise) curve in the position domain can only be done at
the expense of a more gradual (less precise) curve in the speed domain,
and vice versa. More sharpness in the position domain requires
contributions from more frequencies in the speed domain to create the
narrower curve, and vice versa. It is a fundamental tradeoff inherent in
any such related or complementary measurements, but is only really noticeable at the smallest (Planck) scale, near the size of elementary particles.
The uncertainty principle shows mathematically that the product of the uncertainty in the position and momentum
of a particle (momentum is velocity multiplied by mass) could never be
less than a certain value, and that this value is related to the Planck constant.
Wave function collapse means that a measurement has forced or
converted a quantum (probabilistic or potential) state into a definite
measured value. This phenomenon is only seen in quantum mechanics rather
than classical mechanics.
For example, before a photon actually "shows up" on a detection
screen it can be described only with a set of probabilities for where it
might show up. When it does appear, for instance in the CCD
of an electronic camera, the time and space where it interacted with
the device are known within very tight limits. However, the photon has
disappeared in the process of being captured (measured), and its quantum
wave function
has disappeared with it. In its place, some macroscopic physical change
in the detection screen has appeared, e.g., an exposed spot in a sheet
of photographic film, or a change in electric potential in some cell of a
CCD.
Because of the uncertainty principle, statements about both the position and momentum of particles can assign only a probability
that the position or momentum has some numerical value. Therefore, it
is necessary to formulate clearly the difference between the state of
something indeterminate, such as an electron in a probability cloud, and
the state of something having a definite value. When an object can
definitely be "pinned-down" in some respect, it is said to possess an eigenstate.
In the Stern–Gerlach experiment discussed above,
the quantum model predicts two possible values of spin for the atom
compared to the magnetic axis. These two eigenstates are named
arbitrarily 'up' and 'down'. The quantum model predicts these states
will be measured with equal probability, but no intermediate values will
be seen. This is what the Stern–Gerlach experiment shows.
The eigenstates of spin about the vertical axis are not
simultaneously eigenstates of spin about the horizontal axis, so this
atom has an equal probability of being found to have either value of
spin about the horizontal axis. As described in the section above,
measuring the spin about the horizontal axis can allow an atom that was
spun up to spin down: measuring its spin about the horizontal axis
collapses its wave function into one of the eigenstates of this
measurement, which means it is no longer in an eigenstate of spin about
the vertical axis, so can take either value.
In 1924, Wolfgang Pauli proposed a new quantum degree of freedom (or quantum number),
with two possible values, to resolve inconsistencies between observed
molecular spectra and the predictions of quantum mechanics. In
particular, the spectrum of atomic hydrogen had a doublet, or pair of lines differing by a small amount, where only one line was expected. Pauli formulated his exclusion principle,
stating, "There cannot exist an atom in such a quantum state that two
electrons within [it] have the same set of quantum numbers."
In 1928, Paul Dirac extended the Pauli equation, which described spinning electrons, to account for special relativity.
The result was a theory that dealt properly with events, such as the
speed at which an electron orbits the nucleus, occurring at a
substantial fraction of the speed of light. By using the simplest electromagnetic interaction,
Dirac was able to predict the value of the magnetic moment associated
with the electron's spin and found the experimentally observed value,
which was too large to be that of a spinning charged sphere governed by classical physics. He was able to solve for the spectral lines of the hydrogen atom and to reproduce from physical first principles Sommerfeld's successful formula for the fine structure of the hydrogen spectrum.
Dirac's equations sometimes yielded a negative value for energy,
for which he proposed a novel solution: he posited the existence of an antielectron and a dynamical vacuum. This led to the many-particle quantum field theory.
In quantum physics, a group of particles can interact or be created together in such a way that the quantum state
of each particle of the group cannot be described independently of the
state of the others, including when the particles are separated by a
large distance. This is known as quantum entanglement.
An early landmark in the study of entanglement was the Einstein–Podolsky–Rosen (EPR) paradox, a thought experiment proposed by Albert Einstein, Boris Podolsky and Nathan Rosen which argues that the description of physical reality provided by quantum mechanics is incomplete. In a 1935 paper titled "Can Quantum-Mechanical Description of Physical
Reality be Considered Complete?", they argued for the existence of
"elements of reality" that were not part of quantum theory, and
speculated that it should be possible to construct a theory containing
these hidden variables.
The thought experiment involves a pair of particles prepared in
what would later become known as an entangled state. Einstein, Podolsky,
and Rosen pointed out that, in this state, if the position of the first
particle were measured, the result of measuring the position of the
second particle could be predicted. If instead the momentum of the first
particle were measured, then the result of measuring the momentum of
the second particle could be predicted. They argued that no action taken
on the first particle could instantaneously affect the other, since
this would involve information being transmitted faster than light,
which is forbidden by the theory of relativity.
They invoked a principle, later known as the "EPR criterion of
reality", positing that: "If, without in any way disturbing a system, we
can predict with certainty (i.e., with probability
equal to unity) the value of a physical quantity, then there exists an
element of reality corresponding to that quantity." From this, they
inferred that the second particle must have a definite value of both
position and of momentum prior to either quantity being measured. But
quantum mechanics considers these two observables incompatible
and thus does not associate simultaneous values for both to any system.
Einstein, Podolsky, and Rosen therefore concluded that quantum theory
does not provide a complete description of reality. In the same year, Erwin Schrödinger used the word "entanglement" and declared: "I would not call that one but rather the characteristic trait of quantum mechanics."
The Irish physicist John Stewart Bell
carried the analysis of quantum entanglement much further. He deduced
that if measurements are performed independently on the two separated
particles of an entangled pair, then the assumption that the outcomes
depend upon hidden variables within each half implies a mathematical
constraint on how the outcomes on the two measurements are correlated.
This constraint would later be named the Bell inequality.
Bell then showed that quantum physics predicts correlations that
violate this inequality. Consequently, the only way that hidden
variables could explain the predictions of quantum physics is if they
are "nonlocal", which is to say that somehow the two particles are able
to interact instantaneously no matter how widely they ever become
separated. Performing experiments like those that Bell suggested, physicists have
found that nature obeys quantum mechanics and violates Bell
inequalities. In other words, the results of these experiments are
incompatible with any local hidden variable theory.
The idea of quantum field theory began in the late 1920s with British physicist Paul Dirac, when he attempted to quantize the energy of the electromagnetic field;
just as in quantum mechanics the energy of an electron in the hydrogen
atom was quantized. Quantization is a procedure for constructing a
quantum theory starting from a classical theory.
Merriam-Webster defines a field in physics as "a region or space in which a given effect (such as magnetism) exists". Other effects that manifest themselves as fields are gravitation and static electricity. In 2008, physicist Richard Hammond wrote:
Sometimes we distinguish between quantum mechanics (QM)
and quantum field theory (QFT). QM refers to a system in which the
number of particles is fixed, and the fields (such as the
electromechanical field) are continuous classical entities. QFT ...
goes a step further and allows for the creation and annihilation of
particles ...
He added, however, that quantum mechanics is often used to refer to "the entire notion of quantum view".
In 1931, Dirac proposed the existence of particles that later became known as antimatter. Dirac shared the Nobel Prize in Physics for 1933 with Schrödinger "for the discovery of new productive forms of atomic theory".
Quantum electrodynamics (QED) is the name of the quantum theory of the electromagnetic force. Understanding QED begins with understanding electromagnetism. Electromagnetism can be called "electrodynamics" because it is a dynamic interaction between electrical and magnetic forces. Electromagnetism begins with the electric charge.
Electric charges are the sources of and create, electric fields.
An electric field is a field that exerts a force on any particles that
carry electric charges, at any point in space. This includes the
electron, proton, and even quarks,
among others. As a force is exerted, electric charges move, a current
flows, and a magnetic field is produced. The changing magnetic field, in
turn, causes electric current (often moving electrons). The physical description of interacting charged particles, electrical currents, electrical fields, and magnetic fields is called electromagnetism.
In 1928 Paul Dirac produced a relativistic quantum theory of
electromagnetism. This was the progenitor to modern quantum
electrodynamics, in that it had essential ingredients of the modern
theory. However, the problem of unsolvable infinities developed in this relativistic quantum theory. Years later, renormalization
largely solved this problem. Initially viewed as a provisional, suspect
procedure by some of its originators, renormalization eventually was
embraced as an important and self-consistent tool in QED and other
fields of physics. Also, in the late 1940s Feynman diagrams
provided a way to make predictions with QED by finding a probability
amplitude for each possible way that an interaction could occur. The
diagrams showed in particular that the electromagnetic force is the
exchange of photons between interacting particles.
The Lamb shift
is an example of a quantum electrodynamics prediction that has been
experimentally verified. It is an effect whereby the quantum nature of
the electromagnetic field makes the energy levels in an atom or ion
deviate slightly from what they would otherwise be. As a result,
spectral lines may shift or split.
Similarly, within a freely propagating electromagnetic wave, the current can also be just an abstract displacement current, instead of involving charge carriers. In QED, its full description makes essential use of short-lived virtual particles. There, QED again validates an earlier, rather mysterious concept.
The physical measurements, equations, and predictions pertinent to
quantum mechanics are all consistent and hold a very high level of
confirmation. However, the question of what these abstract models say
about the underlying nature of the real world has received competing
answers. These interpretations are widely varying and sometimes somewhat
abstract. For instance, the Copenhagen interpretation states that before a measurement, statements about a particle's properties are completely meaningless, while the many-worlds interpretation describes the existence of a multiverse made up of every possible universe.
Light behaves in some aspects like particles and in other aspects
like waves. Matter—the "stuff" of the universe consisting of particles
such as electrons and atoms—exhibits wavelike behavior too. Some light sources, such as neon lights,
give off only certain specific frequencies of light, a small set of
distinct pure colors determined by neon's atomic structure. Quantum
mechanics shows that light, along with all other forms of electromagnetic radiation, comes in discrete units, called photons, and predicts its spectral energies (corresponding to pure colors), and the intensities of its light beams. A single photon is a quantum,
or smallest observable particle, of the electromagnetic field. A
partial photon is never experimentally observed. More broadly, quantum
mechanics shows that many properties of objects, such as position,
speed, and angular momentum,
that appeared continuous in the zoomed-out view of classical mechanics,
turn out to be (in the very tiny, zoomed-in scale of quantum mechanics)
quantized. Such properties of elementary particles
are required to take on one of a set of small, discrete allowable
values, and since the gap between these values is also small, the
discontinuities are only apparent at very tiny (atomic) scales.
The relationship between the frequency of electromagnetic radiation and the energy of each photon is why ultraviolet light can cause sunburn, but visible or infrared light cannot. A photon of ultraviolet light delivers a high amount of energy—enough
to contribute to cellular damage such as occurs in a sunburn. A photon
of infrared light delivers less energy—only enough to warm one's skin.
So, an infrared lamp can warm a large surface, perhaps large enough to
keep people comfortable in a cold room, but it cannot give anyone a
sunburn.
In even a simple light switch, quantum tunneling is absolutely vital, as otherwise the electrons in the electric current could not penetrate the potential barrier made up of a layer of oxide. Flash memory chips found in USB drives also use quantum tunneling, to erase their memory cells.
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 organic 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 Greekμύκης, mykes'mushroom'). In the past, mycology was regarded as a branch of botany, although it is now known that fungi are genetically more closely related to animals than to plants.
Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting,
either as mushrooms or as molds. Fungi perform an essential role in the
decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment. They have long been used as a direct source of human food, in the form of mushrooms and truffles; as a leavening agent for bread; and in the fermentation of various food products, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control weeds, plant diseases, and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals, including humans. The fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g., rice blast disease) or food spoilage can have a large impact on human food supplies and local economies.
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of the fungus kingdom, which has been estimated at 2.2 million to 3.8 million species. Of these, only about 148,000 have been described, with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. Ever since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christiaan Hendrik Persoon, and Elias Magnus Fries,
fungi have been classified according to their morphology (e.g.,
characteristics such as spore color or microscopic features) or physiology. Advances in molecular genetics have opened the way for DNA analysis
to be incorporated into taxonomy, which has sometimes challenged the
historical groupings based on morphology and other traits. Phylogenetic
studies published in the first decade of the 21st century have helped
reshape the classification within the fungi kingdom, which is divided
into one subkingdom, seven phyla, and ten subphyla.
Etymology
The English word fungus is directly adopted from the Latinfungus'mushroom', used in the writings of Horace and Pliny. This in turn is derived from the Greek word sphongos (σφόγγος'sponge'), which refers to the macroscopic structures and morphology of mushrooms and molds; the root is also used in other languages, such as the German Schwamm'sponge' and Schimmel'mold'.
The word mycology is derived from the Greek mykes (μύκης'mushroom') and logos (λόγος'discourse'). It denotes the scientific study of fungi. The Latin adjectival form of "mycology" (mycologicæ) appeared as early as 1796 in a book on the subject by Christiaan Hendrik Persoon. The word appeared in English as early as 1824 in a book by Robert Kaye Greville. In 1836 the English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward Smith, Vol. 5. also refers to mycology as the study of fungi.
A group of all the fungi present in a particular region is known as mycobiota (plural noun, no singular). The term mycota is often used for this purpose, but many authors use it as a synonym of Fungi. The word funga has been proposed as a less ambiguous term morphologically similar to fauna and flora. The Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN) in August 2021 asked that the phrase fauna and flora be replaced by fauna, flora, and funga.
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 habit. Although
inaccurate, the common misconception that fungi are plants persists
among the general public due to their historical classification, as well
as several similarities. Like plants, fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit bodies, which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago (around the start of the Neoproterozoic Era). Some morphological, biochemical, and genetic features are shared with
other organisms, while others are unique to the fungi, clearly
separating them from the other kingdoms:
With 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.
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.
Some species grow as unicellular yeasts that do not form hyphae and 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.
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 themselves 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
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 2,000 with a peak
of more than 2,500 species in 2016. In the year 2019, 1,882 new species
of fungi were described, and it was estimated that more than 90% of
fungi remain unknown. The following year, 2,905 new species were described—the highest annual record of new fungus names. In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy. Species may also be distinguished by their biochemical and physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to chemical tests. The biological species concept discriminates species based on their ability to mate. The application of molecular tools, such as DNA sequencing and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates of genetic diversity within various taxonomic groups.
Mycology 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.
Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10μm
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 and blastocladiomycetes 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.
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 900ha (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 Purpureocillium lilacinum uses a similar structure to penetrate the eggs of nematodes.
The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol. Adaptations such as these are complemented by hydrolytic enzymes secreted into the environment to digest large organic molecules—such as polysaccharides, proteins, and lipids—into smaller molecules that may then be absorbed as nutrients. The vast majority of filamentous fungi grow in a polar fashion
(extending in one direction) by elongation at the tip (apex) of the
hypha. Other forms of fungal growth include intercalary extension
(longitudinal expansion of hyphal compartments that are below the apex)
as in the case of some endophytic fungi, or growth by volume expansion during the development of mushroom stipes and other large organs. Growth of fungi as multicellular structures consisting of somatic and reproductive cells—a feature independently evolved in animals and plants—has several functions, including the development of fruit bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication.
Fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixed by other organisms for metabolism. Fungi have evolved
a high degree of metabolic versatility that allows them to use a
diverse range of organic substrates for growth, including simple
compounds such as nitrate, ammonia, acetate, or ethanol. In some species the pigment melanin may play a role in extracting energy from ionizing radiation, such as gamma radiation. This form of "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlying biophysical and biochemical processes are not well known. This process might bear similarity to CO2 fixation via visible light, but instead uses ionizing radiation as a source of energy.
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 with meiosis has been directly observed in all fungal phyla except Glomeromycota (genetic analysis suggests meiosis in Glomeromycota as well). It
differs in many aspects from sexual reproduction in animals or plants.
Differences also exist between fungal groups and can be used to
discriminate species by morphological differences in sexual structures
and reproductive strategies. Mating experiments between fungal isolates may identify species on the basis of biological species concepts. The major fungal groupings have initially been delineated based on the
morphology of their sexual structures and spores; for example, the
spore-containing structures, asci and basidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Fungi employ two mating systems: heterothallic species allow mating only between individuals of the opposite mating type, whereas homothallic species can mate, and sexually reproduce, with any other individual or itself.
Most fungi have both a haploid and a diploid
stage in their life cycles. In sexually reproducing fungi, compatible
individuals may combine by fusing their hyphae together into an
interconnected network; this process, anastomosis, is required for the initiation of the sexual cycle. Many ascomycetes and basidiomycetes go through a dikaryotic
stage, in which the nuclei inherited from the two parents do not
combine immediately after cell fusion, but remain separate in the hyphal
cells (see heterokaryosis).
In ascomycetes, dikaryotic hyphae of the hymenium (the spore-bearing tissue layer) form a characteristic hook (crozier) at the hyphal septum. During cell division,
the formation of the hook ensures proper distribution of the newly
divided nuclei into the apical and basal hyphal compartments. An ascus
(plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. Asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. After dispersal, the ascospores may germinate and form a new haploid mycelium.
Sexual reproduction in basidiomycetes is similar to that of the
ascomycetes. Compatible haploid hyphae fuse to produce a dikaryotic
mycelium. However, the dikaryotic phase is more extensive in the
basidiomycetes, often also present in the vegetatively growing mycelium.
A specialized anatomical structure, called a clamp connection,
is formed at each hyphal septum. As with the structurally similar hook
in the ascomycetes, the clamp connection in the basidiomycetes is
required for controlled transfer of nuclei during cell division, to
maintain the dikaryotic stage with two genetically different nuclei in
each hyphal compartment. A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis. The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).
In fungi formerly classified as Zygomycota, haploid hyphae of two individuals fuse, forming a gametangium, a specialized cell structure that becomes a fertile gamete-producing cell. The gametangium develops into a zygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which may then form asexual sporangiospores.
These sporangiospores allow the fungus to rapidly disperse and
germinate into new genetically identical haploid fungal mycelia.
Spore dispersal
The spores of most of the researched species of fungi are transported by wind.Such species often produce dry or hydrophobic spores that do not absorb water and are readily scattered by raindrops, for example.In other species, both asexual and sexual spores or sporangiospores are
often actively dispersed by forcible ejection from their reproductive
structures. This ejection ensures exit of the spores from the
reproductive structures as well as traveling through the air over long
distances.
Specialized mechanical and physiological mechanisms, as well as spore surface structures (such as hydrophobins), enable efficient spore ejection. For example, the structure of the spore-bearing cells in some ascomycete species is such that the buildup of substances affecting cell volume and fluid balance enables the explosive discharge of spores into the air. The forcible discharge of single spores termed ballistospores
involves formation of a small drop of water (Buller's drop), which upon
contact with the spore leads to its projectile release with an initial
acceleration of more than 10,000g; 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.
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.
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. The oldest fossilizied mycelium to be identified from its molecular composition is between 715 and 810 million years old. For much of the Paleozoic Era (542–251Ma), 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 possibly 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".
External phylogeny
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).
Internal phylogeny
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 subkingdomDikarya,
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.
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 sedisMucoromycotina, Kickxellomycotina, the Zoopagomycotina and the Entomophthoromycotina. Some well-known examples of fungi formerly in the Zygomycota include black bread mold (Rhizopus stolonifer), and Pilobolus species, capable of ejecting spores several meters through the air. Medically relevant genera include Mucor, Rhizomucor, and Rhizopus.
The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota. These fungi form meiotic spores called ascospores, which are enclosed in a special sac-like structure called an ascus. This phylum includes morels, a few mushrooms and truffles, unicellular yeasts (e.g., of the genera Saccharomyces, Kluyveromyces, Pichia, and Candida),
and many filamentous fungi living as saprotrophs, parasites, and
mutualistic symbionts (e.g. lichens). Prominent and important genera of
filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), but analysis of molecular data has often been able to identify their closest teleomorphs in the Ascomycota. Because the products of meiosis are retained within the sac-like ascus,
ascomycetes have been used for elucidating principles of genetics and
heredity (e.g., Neurospora crassa).
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 Rozellida clade, including the "ex-chytrid" Rozella, is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi. Members of the group that have been isolated lack the chitinous cell wall that is characteristic of fungi. Alternatively, Rozella can be classified as a basal fungal group.
The nucleariids may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom. Many Actinomycetales (Actinomycetota), a group with many filamentous bacteria, were also long believed to be fungi.
Ecology
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 aquatic ecosystems, and therefore play a critical role in biogeochemical cycles and in many food webs. As decomposers, they play an essential role in nutrient cycling, especially as saprotrophs and symbionts, degrading organic matter to inorganic molecules, which can then re-enter anabolic metabolic pathways in plants or other organisms.
Symbiosis
Many fungi have important symbiotic relationships with organisms from most if not all kingdoms. These interactions can be mutualistic or antagonistic in nature, or in the case of commensal fungi are of no apparent benefit or detriment to the host.
With plants
Mycorrhizal symbiosis between plants
and fungi is one of the most well-known plant–fungus associations and
is of significant importance for plant growth and persistence in many
ecosystems; over 90% of all plant species engage in mycorrhizal
relationships with fungi and are dependent upon this relationship for
survival.
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.
Lichens are a symbiotic relationship between fungi and photosyntheticalgae or cyanobacteria.
The photosynthetic partner in the relationship is referred to in lichen
terminology as a "photobiont". The fungal part of the relationship is
composed mostly of various species of ascomycetes and a few basidiomycetes. Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession, and are prominent in some extreme environments, including polar, alpine, and semiarid desert regions. They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves. As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis
to the fungus, while the fungus provides minerals and water to the
photobiont. The functions of both symbiotic organisms are so closely
intertwined that they function almost as a single organism; in most
cases the resulting organism differs greatly from the individual
components. Lichenization is a common mode of nutrition for fungi; around 27% of known fungi—more than 19,400 species—are lichenized. Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of desiccation than most other photosynthetic organisms in the same habitat.
With insects
Many insects also engage in mutualistic relationships with fungi. Several groups of ants cultivate fungi in the order Chaetothyriales
for several purposes: as a food source, as a structural component of
their nests, and as a part of an ant/plant symbiosis in the domatia (tiny chambers in plants that house arthropods). Ambrosia beetles cultivate various species of fungi in the bark of trees that they infest. Likewise, females of several wood wasp species (genus Sirex) inject their eggs together with spores of the wood-rotting fungus Amylostereum areolatum into the sapwood of pine trees; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae. At least one species of stingless bee has a relationship with a fungus in the genus Monascus, where the larvae consume and depend on fungus transferred from old to new nests. Termites on the African savannah are also known to cultivate fungi, and yeasts of the genera Candida and Lachancea inhabit the gut of a wide range of insects, including neuropterans, beetles, and cockroaches; it is not known whether these fungi benefit their hosts. Fungi growing in dead wood are essential for xylophagous insects (e.g. woodboring beetles). They deliver nutrients needed by xylophages to nutritionally scarce dead wood. Thanks to this nutritional enrichment the larvae of the woodboring insect is able to grow and develop to adulthood. The larvae of many families of fungicolous flies, particularly those within the superfamily Sciaroidea such as the Mycetophilidae and some Keroplatidae feed on fungal fruiting bodies and sterile mycorrhizae.
Many fungi are parasites
on plants, animals (including humans), and other fungi. Serious
pathogens of many cultivated plants causing extensive damage and losses
to agriculture and forestry include the rice blast fungus Magnaporthe oryzae, tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi causing Dutch elm disease, Cryphonectria parasitica responsible for chestnut blight, and Phymatotrichopsis omnivora causing Texas Root Rot, and plant pathogens in the genera Fusarium, Ustilago, Alternaria, and Cochliobolus. Some carnivorous fungi, like Purpureocillium lilacinum, 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.
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
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.
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.
Many fungi produce biologically active compounds, several of which are toxic to animals or plants and are therefore called mycotoxins.
Of particular relevance to humans are mycotoxins produced by molds
causing food spoilage, and poisonous mushrooms (see above). Particularly
infamous are the lethal amatoxins in some Amanita mushrooms, and ergot alkaloids, which have a long history of causing serious epidemics of ergotism (St Anthony's Fire) in people consuming rye or related cereals contaminated with sclerotia of the ergot fungus, Claviceps purpurea. Other notable mycotoxins include the aflatoxins, which are insidious liver toxins and highly carcinogenic metabolites produced by certain Aspergillus species often growing in or on grains and nuts consumed by humans, ochratoxins, patulin, and trichothecenes (e.g., T-2 mycotoxin) and fumonisins, which have significant impact on human food supplies or animal livestock.
Mycotoxins are secondary metabolites (or natural products),
and research has established the existence of biochemical pathways
solely for the purpose of producing mycotoxins and other natural
products in fungi. Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory). Many fungal secondary metabolites (or derivatives) are used medically, as described under Human use below.
Pathogenic mechanisms
Ustilago maydis is a pathogenic plant fungus that causes smut disease in maize and teosinte. Plants have evolved efficient defense systems against pathogenic microbes such as U. maydis. A rapid defense reaction after pathogen attack is the oxidative burst where the plant produces reactive oxygen species at the site of the attempted invasion. U. maydis can respond to the oxidative burst with an oxidative stress response, regulated by the gene YAP1. The response protects U. maydis from the host defense, and is necessary for the pathogen's virulence. Furthermore, U. maydis has a well-established recombinational DNA repair system which acts during mitosis and meiosis. The system may assist the pathogen in surviving DNA damage arising from
the host plant's oxidative defensive response to infection.
Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals. C.neoformans usually infects the lungs, where it is phagocytosed by alveolar macrophages. Some C.neoformans can survive inside macrophages, which appears to be the basis for latency, disseminated disease, and resistance to antifungal agents. One mechanism by which C.neoformans
survives the hostile macrophage environment is by up-regulating the
expression of genes involved in the oxidative stress response. Another mechanism involves meiosis. The majority of C.neoformans
are mating "type a". Filaments of mating "type a" ordinarily have
haploid nuclei, but they can become diploid (perhaps by endoduplication
or by stimulated nuclear fusion) to form blastospores.
The diploid nuclei of blastospores can undergo meiosis, including
recombination, to form haploid basidiospores that can be dispersed. This process is referred to as monokaryotic fruiting. This process requires a gene called DMC1, which is a conserved homologue of genes recA in bacteria and RAD51 in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus, C.neoformans
can undergo a meiosis, monokaryotic fruiting, that promotes
recombinational repair in the oxidative, DNA damaging environment of the
host macrophage, and the repair capability may contribute to its
virulence.
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.
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.
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.).
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.
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 Conocybe, Galerina, Lepiota and the most infamous, Amanita. The latter genus includes the destroying angel (A.virosa) and the death cap (A.phalloides), the most common cause of deadly mushroom poisoning. The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw. Tricholoma equestre was considered edible until 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.
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 Epichloë, 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.
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