Fungus
Fungi
Fagus mycorhiza
Fungal hypha
Above: a bracket fungus. These fungi are usually found on the sides of trees and on fallen logs. This
one is probably growing on a decomposing log beneath the soil surface. Fungi were once classed as
plants, but they do not photosynthesise, but instead obtain nourishment from preformed organic
materials, in much the same way that animals do. Many are
saprotrophic - feeding off decomposing
organic remains, such as dead wood. Some are parasitic and may feed off the living tissues of plants
(and sometimes animals). Others exist in harmonious symbiosis with organisms that can
photosynthesise. Most trees require such fungal
symbionts if they are to grow properly (especially on
poorer soils). These fungi associate with plant roots, forming
mycorhizae (or mycorhizas, lit. 'fungus
roots', sing.
mycorhiza). The body of a fungus is an often large and diffuse mass of whitish hairlike
threads that spread through soil, rotting logs or living wood in the case of parasites. This mass is called
the
mycelium. The part of the fungus that is usually visible are the sporocarps or sporing bodies, like
those shown above. Periodically the mycelium puts out these structures into the open to shed spores.
The mycelium is made up of fine hairlike fibres called
hyphae. Hyphae have a very large surface area
to volume ratio, which makes them exceptionally good at absorbing nutrients. The hyphae secrete
enzymes (or rely on those secreted by other micro-organisms) into their food, digesting it and then
absorbing the nutrients with their hyphae. In the case of mycelia, the hyphae are especially good at
absorbing hard-to-get soil nutrients like phosphorus, indeed they are much better than plant roots at
this. They give the plant roots some of these minerals in exchange for sugars manufactured by the
plant during photosynthesis.

The diagram below shows the mycorhiza of the beech tree (
Fagus sylvatica). The mycelium forms a
hairlike net that en-sheaths part of the root, this is called the
Hartig net. Some of these hyphae
penetrate between the root epidermal cells, which form the outer layer of root tissue.
A single fungus may, in this way, connect the roots of several trees together. The roots of neighbouring
trees may also naturally graft directly together, especially if the trees belong to the same species. Such
grafted roots can exchange nutrients and this helps the weaker trees. If a tree is felled, the stump may
regenerate (depending on the species) by putting out new shoots. Some of the nutrients for this growth may
come from neighbouring trees through the interconnected root network.

The
largest organism on Earth is thought to be a fungus, whose mycelium covers some 37 acres, is
estimated to be about 700 years old and to weigh over 100 tonnes. However, it is not easy to prove whether
this mycelium remains continuous or whether it has fragmented into several smaller mycelia (which would
make it a clone rather than a single organism).

Some fungi can form mycorhizas with a variety of different trees, but each woodland type, such as beech,
birch, oak or pine, has its own characteristic set of mycorhizal fungi. For example, the fly agaric,
Amanita
muscaria
, will only grow under birch and pine. Likewise, each species of tree is often capable of forming
mycorhizas with several different fungus species. These fungi may or may not contribute to leaf litter
decomposition, but they are good at extracting nutrients like phosphate. Brushing aside the leaf-litter in a
beechwood will reveal the tiny feeder roots that protrude vertically into the leaf-litter and these coral-like
roots are the mycorhizas.

Orchids characteristically form mycorhizas of a type called
endomycorhizas - in this type there is no
external hyphal sheath, or Hartig net, around the root, and the fungal hyphae penetrate and internally
invade the cells in the outer layers of the root. Deeper in the root is a zone in which cells are digesting the
fungal hyphae and the central zone is fungus-free. These fungi can digest cellulose and lignin (present in
plant remains) and the relationship appears a complex and unsettled one. The orchids need the mycorhizas
when they are young germlings and seedlings. The seeds will not germinate without their fungal partner,
however, sometimes the fungus infects and consumes the seed, destroying it. This illustrates how these
mutualistic symbioses cover a spectrum of relationships, with the fungus parasitising the plant on one hand,
and the plant eating the fungus on the other. Some orchids are non-photosynthetic and  lack green
chlorophyll and these depend on their fungal partner to provide them food throughout their life. In contrast
to the mycorhizas of trees, in which the fungus provides minerals and the plant sugars, in orchid mycorhizas
the fungus appears to be supplying the plant with sugars by digesting cellulose. In this way many orchids
are able to feed saprotrophically as well as photosynthetically. Many other herbaceous plants rely on
mycorhizas, but mycorhizas tend to be absent from grassland.
Key
Left: the growing tip of a fungal hypha. Hyphae grow at their
tips. The fungus 'cell' is really a giant cell with many nuclei,
though in some fungi cross-wall partitions occur at intervals
along the hypha. The hypha is surrounded by a hyphal wall.
the growing tip is rich in vesicles, which either bud from the
Golgi apparatus (dictyosomes) if these are present, or else
directly from the endoplasmic reticulum. Many of these
vesicles fuse with the cell-surface membrane at the hyphal tip
and discharge their cargo by exocytosis, which will include
materials to extend the cell wall as the hypha grows. The
vesicles also add to the cell-surface membrane.

Behind this zone is a region of intense metabolic activity -
rich in ribosomes that synthesise proteins and mitochondria
that provide the hypha with power.

Further from the tip, vacuoles of increasing size become
increasingly numerous and large lipid bodies which store fuel.

The middle zone, rich in ribosomes, may be much longer
than illustrated here.

Fungi (properly pronounced 'fun-gee' with a hard g as is
'geyser') take a very different approach to the cellular
animals and plants, in that they build bodies from hyphal
filaments. The hyphae often have cross-walls, with pores
connecting the cytoplasm on either side, and so can in this
case be considered as chains of cellular units. However,
although we sometimes refer to fungal cells, with the
exception of the cellular yeasts, it is not always easy to say
what exactly a fungal 'cell' is: is it a hypha or one unit in a
hypha partitioned by cross-walls.
Mushroom pseudoparenchyma
Left: a cross-section through part of
stalk is made up of columns of hyphae,
of variable size, packed together. In
cross-section these hyphae resemble
the
parenchyma cells of plants, but in
longitudinal section are shown to be
long filaments, unlike parenchyma, and
so are sometimes called
pseudoparenchyma. This is an
interesting alternative approach to
building a body - building it from
filaments. These sporing or fruiting
bodies, such as toadstools, enable
spores to be released above the
boundary layer of still air that coats
solid surfaces. In air the boundary
layer is generally much thicker than in
flowing water. In water microscopic
filaments or
biofilms may be sufficient
to break the boundary layer.
One of the most remarkable things about fungi is their hardiness. Fungi have been able to colonise
extreme environments, such as inside rocks in the extremely cold and dry Antarctic deserts (the driest
places on Earth) and the inside of fuel tanks. Even the mildew that may grow on walls and other damp
surfaces seems to grow well with remarkably little. Many fungi are colonisers, some are adapted to grow
on burnt soil in forests, and their spores will only germinate in high temperatures. Lichens can grow on
bare rocks, even on wind-blasted and salty rocks that line the upper shores. Lichens are remarkable
composite organisms - composed of two very different organisms growing in a single body. One is the
fungus, the other is a photosynthetic cyanobacterium or a eukaryotic alga.
Above: Daldinia (probably Daldinia concentrica) otherwise known as King Alfred's Cakes. This fungud
grows on ash and occasionally on other deciduous trees. Here it is growing on a fallen branch, which
does look like ash. The sporing body can be up to 5 cm (2 inches) across. Also sporulating on this log
was a myxomycete or plasmodial
slime mould.
More Fungi

Types of Fungi

Fungi are classified scientifically into several groups and can also be classified more commonly by
general appearance. Scientifically we recognise three major divisions: 1) zygomycetes, 2) ascomycetes,
and 3) basidiomycetes.

1) The
zygomycetes are the simplest of the true fungi, and many moulds belong to this group (moulds
can also be bacterial or protoctistan in origin, see classification of organisms). These moulds consist of
spreading masses of feeding hairlike-hyphae (the mycelium) and vertical
aerial hyphae, such as the
sporangiophores, bearing sporing bodies/capsules (sporangia, sing. sporangium) which contain a
mass of spores. The mycelium consists of branching hyphae that generally lack dividing cross-walls (they
are aseptate), so that they are multinucleate and the protoplasm is undivided. Cross-walls do form in old
colonies, however, where they wall off dead air-filled hyphae from the still living hyphae.

Reproduction in Zygomycetes

Bread mould, Mucor, is a common example. Mucor is heterothallic, meaning it exists in two body types
(heterothallic = more than one 'body' or thallus type) which are physically identical but of different sexual
compatibilities: the + (plus) type of mycelium can only mate with a - (minus) type of mycelium and vice
versa - mycelia of like types can not mate. Each spore produces either a plus-type or a minus-type
mycelium, upon germinating. Each mycelium produces minute, more-or-less spherical,
asexual
sporangia
, borne on sporangiophore stalks and the asexual spores are of the same genetic type as the
parent mycelium (they are genetic clones of the parent). A hemispherical cross-wall, called the columella,
forms the wall of the sporangium and divides the sporangiophore stalk from the sporangium.
This bracket fungus, growing on an oak tree, is probably
Ishnoderma resinosum or a related form, as it has the right
shape and colour and characteristically yields drops of red
resin (click photos to enlarge, the droplets are visible as
spots). However, this fungus is said to grow on dead
stumps from September to December, but here it is in June
on a living oak tree. Of course it could be feeding off dead
wood that is part of the tree.
Pilobolous mould with eyes, computer model rendered in Pov-Ray
Above: Pilobolus, showing four sporangiophores terminating in the eye-like structure with
lens and yellow ring-shaped retina underneath. A black spore mass sits on top of each
eye, waiting to be fired clear and so disperse the fungus.
The sporangium cap is fired by hydrostatic pressure - the sporangiophore protoplasm builds up some 5
atmospheres of osmotic pressure, swelling with liquid as it does so, until it splits along a pre-determined
line of weakness behind the black cap which is squirted into the air as teh stretched elastic wall of the
sporangiophore recoils. The spore mass or sporangium is discharged along with a droplet of liquid
(mucilage) which sticks to a solid substrate, such as a blade a grass, and the unwettable sporangium
floats to the surface of the droplet before the mucilage hardens to fasten the sporangium to the
substrate. The spore mass is still covered by the dark wall of the sporangium, which probably protects
the spores from UV radiation.

2)
Ascomycetes generally produce larger sporing bodies, typically from several millimetres to several
centimetres in size. They are easily found in woods and forests. They include the disc-fungi and
cup-fungi (
discomycetes) such as the orange-peel fungus, Aleuria aurantia, whose irregular cups
resemble orange-peel and may be up to 8 to 10 cm in diameter and is found growing on bare soil in
woods. This group also includes various flask-fungi and the burnt-fungi, which may be encrusting,
flattened or ball-shaped black structures typically found on dead wood, often dry and brittle when mature,
as if wood had been burnt, such as
Daldinia, shown above, and Hypoxylon; and also various pin-fungi,
resembling fields of pin-heads, often brightly coloured, such as
Nectria cinnabarina, which forms fields of
brownish-red 'pinheads' each 1 - 4 mm across on dead and dying wood.
Xylaria hypoxylon is the candle
snuff fungus, often found in woodlands growing on dead wood. This fungus forms sporing bodes that are
antler-shaped, 3-5 cm tall and have the appearance of snuffed-out candle wicks. The sporing body
consists of one or many minute cylindrical or flask-shaped structures called
asci (sing. ascus) each with
a pore or
ostium in its tip. The asci are modified hyphal hairs and are often accompanied by sterile hairs
called
paraphyses. The spores, called ascospores, develop inside these asci, and are released
through the ostium. The spores are forcefully discharged by a build-up of hydrostatic pressure which
ruptures the asci. For example, in the orange-peel fungus, many cylindrical asci, each about 200
micrometres tall and 10 micrometres wide, line the inside surface of the cup, each opens by an ostium, so
the lining of the cup is porous and spores are fired from these pores, clear of the cup.

Lichens are composite organisms, consisting of a fungal body living along with a photosynthetic algal
partner, which is enclosed in the fungal tissues. The alga may be a simple eukaryotic alga, or a
cyanobacterium. Whilst the alga also occurs in nature living alone, the fungus can not live without its
fungal host. The alga supplied the lichen with sugars produced by photosynthesis and, in the case of
cyanobacteria, with fixed nitrogen. In return the alga is given a protected environment which is elevated
higher above the substrate and so closer to the light. The fungus uses the sugars perhaps as a
carbohydrate and energy source and also as an osmolyte to resist desiccation in those lichens growing
in the splash zone of coastal habitats. The fungal partner is usually an ascomycete, and lichens can be
seen to produce tiny cups which contain typical asci. However, there are so many lichens that they are
usually considered separately.

The mycelium of ascomycetes consists of branching hyphae that also anastomose (fues) to form a 3D
network. The hyphae have dividing cross-walls (they are septate) so that each hypha is divided into a
chain of 'cellular' compartments, each containing one to several nuclei. Each cross-wall has a small
central pore, which is large enough for mitochondria to squeeze through, and also nuclei 9albeit more
slowly), so that the ptotoplasm is continuous throughout the hypha. Such cross-walls add mechanical
strength to a hypha and this is likely their prime function.

3)
Basidiomycetes include those fungi with the largest sporing bodies, such as toadstools, mushrooms
and the bracket fungi shown above. The largest brackets may be several feet across and are often
tough, leathery or woody in texture. They also include some of the jelly-fungi, such as the oddly-named
Jew's-ear fungus (
Auricularia auricula-judae) which is gelatinous and translucent and resembles a
brownish human ear.

In addition to these three groups a fourth, the
deuteromycetes, is a dumping-category for fungi that
have only been observed in the asexual stage and either reproduce sexually only rarely or have lost the
ability altogether. Since spore and sporocarp morphology determine whether a fungus is a zygomycete,
ascomycete or basidiomycete, classifying these fungi is difficult. These are also known as the 'imperfect'
fungi.
Penicillium and Aspergillus belong to this group, though some forms do reproduce sexually and
Penicillium is also an ascomycete. Aspergillus niger has never been seen to reproduce sexually.
Penicillium is, of course, the original source of the first discovered antibiotic,
penicillin, which the fungus
secretes to inhibit the growth of competing bacteria, and ultimately to kill them, allowing the fungus to
feed on their remains.

The spores, called basidiospres, are produced externally rather than inside a cell or hypha. Upon
germination they produce haploid mycelia (haploid = containing half the set of genes, or one parental
copy of the gene set) in which all the nuclei are of the same genetic type. This mycelium is called a
monokaryon. Monokaryons come in several mating types and when two compatible types meet, they
fuse to produce a compartment containing two nuclei, one from each momokaryon. This compartment
grows into the mature fungal mycelium, which contains an equal proportion of nuclei of each of the two
types and so is said to be dikaryotic and is called a
dikaryon. The dikaryon is diploid (containing the full
genetic makeup of two parental sets of genes) even though the nuclei do not apparently fuse, so each
nucleus remains haploid. The basidiospores are produced by compartments called basidia. The nucleus
pair in each basidium fuse, forming a diploid nucleus, which then undergoes meiosis, that is they divide to
form four haploid nuclei. These daughter nuclei form the basidiospores, so each basidium produces four
spores (typically).

The mycelium of basidiomycetes consists of branching and anstomosing hyphae that form a 3D network.
Cross-walls divide the hypha into a chain of compartments, each  compartment typically containing two
nuclei in the dikaryon, one in the monokaryon. A large central pore traverses each cross-wall, so that the
protoplasm throughout the hypha is continuous. The wall material around the pore is thickened, forming
a barrel, the whole structure being called a
dolipore. Surrounding each end of the dolipore is a dome of
perforated endoplasmic reticulum, called a
parenthesome. A new cross-wall is laid down each time a
pair of nuclei divide. Typically, there is a bulge in the cell wall, containing protoplasm, on one side of the
hypha at each cross-wall in the dikaryon, called a
clamp connection. Shortly after duplication of the
pair of nuclei in each growing hyphal tip of the dikaryon, a new cross-wall is deposited, maintaining a pair
of nuclei in each compartment. The clamp connection acts as a conduit for a nucleus as following each
cross-wall formation it is essential to sort the nuclei so that the two new daughter compartments contain
two nuclei, one of each genetic type. To prevent compartments forming containing two nuclei of one type
only, the clamp connection acts as a conduit for a nucleus during re-assortment (otherwise the nucleus
would have a hard time passing through the parenthosome and dolipore).

Proto-fungi

In the same way that algae ('protophytes') are no longer classified as plants, protozoa no longer
classified as animals, there are some 'proto-fungi' that are no longer classified as fungi. These include
the water-fungi or water-moulds (
oomycetes) and the plant pathogen Phytophthora. These proto-fungi
produce water-borne motile spores, called zoospores, at some stage in their life-cycle. these zoospores
swim by means of one or more flagella, typically a tinsellated-flagellum (a flafgellum bearing side hairs) is
held out in front and pulls the cell forward, whilst a typical eukaryotic smooth flagellum, trailing behind,
pushes the cell forwards. Both flagella undulate, with waves passing  from the base to the tip. these
prot-fungi were once grouped with the zygomycetes, as a group called the phycomycetes, but are now
officially grouped (dumped!) with the algae and protozoa in the kingdom Protoctista. Other protofungi
(sometimes classed as protozoa) are the
cellular and plasmodial slime-moulds.

Sporocarps

As we have seen, the main body of a fungus is the white mass of very fine branching hyphae, called the
mycelium, which lives beneath or within the substrate on which the fungus grows (such as wood or soil).
The mycelium is the feeding and growing part of the fungus. It removes nutrients and water from the
substrate, by secreting enzymes and then absorbing the released nutrients through its fine hyphae,
which have very large surface area to volume ratios. The mycelium is exceptional at absorbing nutrients,
which is why most trees and other flowering plants rely on mycorhizae for nutrients.

At certain times of the year, the mycelium puts out one or more 'fruit', more properly called sporing
bodies or
sporocarps. The cups, discs, brackets and toadstools we have seen are all sporocarps. A
medium-sized mushroom releases some 500 000 spores a minute over a several day period called
spore fall. Most sporocarps die after spore fall, though some can live for ten years but only spore for a
few weeks each year. Commonly, fungi are often classified by sporocarp type, as follows. This type of
classification is descriptive.

1) Toadstools and mushrooms

Umbrela-shaped with a circular cap supported on a central stalk. Many basidiomycetes have this form.
The cap produces spores, which fall from gill-like slits (as in
Agaricus) or pores (as in Boletus), under
gravity, into the turbulent air, which carries them away. The purpose of the stalk is to raise the cap above
the layer of still air which naturally covers all surfaces, and into the turbulent air layer where the spores
can be better dispersed. Toadstools have a spongy texture and are short-lived, lasting only a few days.
More brackets on a living oak tree.
Boletes, such as Boletus, are toadstools in which instead of gills, the cap has vertical tubes, each
opening by a pore on the underside of the cap. The spores fall from these pores.

2) Bracket Fungi (Shelf Fungi)

Basidiomycetes that grow attached to wood. Some are parasites growing and feeding on living trees.
Others grow on and feed off dead wood, which they help to rot. Sometimes they grow on buried logs and
may then emerge upright as large leathery trumpet-shaped structures that superficially resemble
toadstools. The sporocarps are tough, leathery or woody in texture and may live for 10 years in some
species; they are often large. They are often semicircular and protrude from the log or branch to which
they are attached, like brackets. They have no, or a very short, stalk. Pores on the underside release
spores, which fall under gravity to be dispersed by the wind. Growing attached to wood, they are
naturally elevated above the ground, often at considerable heights if the host tree is still standing, and
so need no stalk to lift them above the still air layers. Some species of bracket fungi are circular (an may
have short stalks) and do not project but are pressed against the wood. In this instance the spores are
released from the upper surface.

3) Stomach fungi

These basidiomycetes are also descriptively called gasteromycetes (literally: 'stomach fungi') and their
sporocarps are sac-like. A well-known example are the
puffballs. Puffball sporocarps consist of spongy
sacs full of spores. The spores are produced by brown tissue, called
gleba, inside the sac and which is
readily visible if a ripe puffball is cut open. There is a single large circular pore, or sometimes a tear, in
the top of the sac. When rain drops hit the sac, they deform it slightly, causing a dense cloud of spores
to be pumped out through the pore (think of a pair of bellows) to a height clear of the stagnant boundary
layer of air. The puffball is elastic and returns to its previous shape, until the next rain drop strikes it. The
falling rain drops provide the energy to disperse the spores, which is due to gravity again.
Giant
puffballs
may be up to 40 cm (16 inches) across and can produce seven million million spores! In the
giant puffball, the spores are released from a tear.

Earth stars are another example of a gasteromycete. Like puffballs, these are sacs of spores and have
one or more pores in the top. The spores are also dispersed by rain-drops, but earthstars can also
move! Leaf-shaped structures or valves close around the sac in dry weather, protecting it and its spores,
and open when wet to allow spore dispersal. These movements are passive and due to tensions set up
in the tissues  which expand to different degrees when wet, expanding most on the outside, causing the
valves to open.

Also belonging to the gasteromycetes are the
bird's nest fungi (Cyathus and Crucibulum) in which the
sporophore consists of a cup or open vase, about 1 centimetre in diameter, and containing disc-like
bodies (
peridiola, sing. peridiolum) or 'eggs' attached to the inner wall of the cup by a small stalk
(funiculus). The whole resembles a tiny bird's nest full of eggs. They occur on rotting wood but
Cyathus
stercoreus
occurs on herbivore dung. The dispersal mechanism is also splash dispersal - large
raindrops striking the inside of the cup are broken into smaller droplets and reflected out of the cup,
often carrying a peridiolum with them for a distance of up to one metre from the cup. The stalk breaks
away from the cup easily and accompanies the peridiolum. The stalk is sticky and attaches the
peridiolum to an object it lands upon. Each peridiolum consists of a wall of hyphal tissue surrounding
gleba (a mass of small chambers separated by tramal tissue and lined by basidia). The hyphae in the
wall may grow out and establish a new colony asexually, but if the peridiolum of
Cyathus stercoreus is
eaten along with vegetation by a herbivore, then the basidiospores pass through and germinate on the
dung.

Sphaerobolus forms tiny cups, only 1-2 millimetres in diameter, containing a single 'egg' or glebal mass
about 1 millimetre in diameter.The cup has two linings, joined at the rim, so that it is like one cup inside
another. The cup is designed to dry out in such a way that strains are set up, until the inner cup
suddenly flips out, bulging up and propelling the glebal mass several metres! The hyphal in the glebal
mass may produce a new mycelium asexually, or sometimes from the basidiospres. Often a new
mycelium grows from large asexual spores called
gemmae, which are also present in the glebal mass.
Again, this fungus may perhaps also be dispersed by herbivores eating the glebal mass and passing te
spores out with their faeces.
toadstool anatomy
3D computer model of a toadstool rendered in Pov-Ray
3D computer model of a toadstool rendered in Pov-Ray
Above: anatomy of a toadstool sporocarp (using a 3D computer model rendered in Pov-Ray). The cap
or pileus
contains gills: flat plates of soft tissue bearing characteristic cells called basidia (singular
basidium). Each basidium initially bears four black spores (basidiospores). These spores are fired away
from the gill surface to a distance of 0.1 to 0.3 millimetres and once clear of the gill they then fall from
the cap, in-between the gill plates, under gravity. Spore discharge is accompanied by shedding of a drop
of liquid from the spore and a weakening of the join connecting the spore to its basidium. Additionally
either surface tension forces and/or electrostatic repulsion are thought to propel the spores from the gill
surface. The
stipe or stalk holds the cap a few centimetres above the surface, placing it above the
most stagnant layer of air (stagnant boundary layer) which is typically a few centimetres, so that when
the spores fall free of the cap they are caught by turbulent air and carried away and dispersed by the
wind.

The
annulus is a disc of tissue where the cap, originally a sphere in the young button-mushroom stage,
was attached to the stipe. When the cap ripens and expands into its umbrella shape, it tears free of the
stipe, leaving the annulus where the breakage occurred. The cap then continues to expand as it
straightens out. Extending from the base of the stipe, into the substrate/soil are fine branching strands,
called
mycelial strands, which are bundles of hyphae. Mycelia often explore the substrate as mycelial
strands and fan out into feeding hyphae where they encounter a food source. Bundling into mycelial
strands helps the mycelium cover larger distances as it grows, and also provide stronger anchorage
points for the sporocarp. The strands are also good at conducting nutrients over large distances from
one part of the mycelium to another. The toadstool is short-lived, lasting a few days. Its light construction
is ideal for its function. Click the thumbnails below for full-size unlabeled versions of the toadstool model.
computer model of mushroom gill modeled in Pov-Ray
computer model of mushroom gill modeled in Pov-Ray, without labels
Above: a vertical section through a mushroom gill (computer
model). The gill comprises a sheet of vertical hyphae, called
the
trama. Either side of this is a sheet of convoluted hyphae,
called the
sub-hymenium, which are more-or-less horizontal
and so appear as
pseudo-parenchyma in section (that as
sections through the width of the hyphae make it appear as if
they are rounded cells, or parenchyma, when they are actually
hyphal threads). Outermost are two layers of
paraphyses (P)
(fleshy hairs) with spore-bearing
basidia (B) dispersed among
them (in a hexagonal arrangement when the gill is seen
face-on, typically with six paraphyses around each basidium,
bottom right) forming the
hymenium. Each basidium produces
four basidiospores, each of which is borne on a small stalk
(
sterigma). When discharged the spores are fires out
sideways in this perspective, before falling down under gravity.
in at least some spaces, it is known that the sterile paraphyses
are in fact developing basidia. The gill is about 150
micrometres thick and each pair of gills are about 100
micrometres apart. Large cells, called
cystidia (sing.
cystidium, not shown) emerge from the hymenium at intervals
and span the gap between neighbouring gills and serve to
keep the gills apart, so that the spores can fall freely.
toadstool gill model seen in surface view
mushroom
mushroom
Bioluminescence

A number of fungi, particularly certain toadstools emit light. The light is frequently emitted by the
sporocarp or spores and may attract nocturnal insects, such as moths, which disperse the spores.
Sometimes the vegetative (non-sexually reproducing) mycelium luminesces. The exact functions of
fungal bioluminescence are not known for certain. Luminescent toadstools are generally wood-eaters,
capable of digesting lignin, a complex polymeric polyphenol which is hard to digest and extremely
resistant to decay.  Since bioluminescence requires a lot of oxygen (requiring a lot of ATP generated by
the mitochondria) it has been suggested that this protects the fungus by consuming reactive oxygen
species (ions, atoms and molecules containing an oxygen radical) produced as toxic by-products of
lignin digestion. The light produced is cold light, as is typical of bioluminescence in which some 90% of
the energy is dissipated as light (compare this to about 10% for a tungsten-filament light-bulb in which
most of the energy is radiated as heat) and the light is green.

Fungal Habitats

Some toadstools found on a damp grass lawn in autumn:
Left: some mushroom graphics for
general purpose use.
Click images to enlarge. These
toadstools were found on a damp lawn
in Autumn.
Marasmius forms classic
'
fairy-rings' - rings of toadstools
growing in a lawn, appearing in the
same place each subsequent year, but
age can be estimated by their
diameter). They occur because as the
mycelium depletes nutrients in the soil
it grows outwards to colonise new soil.
Boletes form mycorrhizae with trees
and are grow in association with tree
roots, which were presumably running
beneath the lawn.
In toadstools not all the gills are of the same size. All the gills extend from the cap margin inwards, but
they are of different lengths. Typically some of the gills extend more-or-less all the way from the margin
to the stipe, these are the largest or primary gills. Between each pair of primary gills is a secondary gill,
which is shorter, extending most of the way towards the stipe, and between each primary and
secondary gill is a short tertiary gill.

Another common toadstool of lawns is the
ink cap (lawyer's wig, shaggy ink cap, or shaggy mane)
Coprinus comatus. This toadstool, which may reach 30 cm in height, is unusual in that the gills, initially
white, turn pink and then black with spores as they drip black ink-like droplets from the gill-margin which
slowly dissolves. These droplets are laden with spores. This happens as the gills undergo
autolysis, or
self-digestion, dissolving into liquid spore masses. They will auto-digest rapidly once picked. In most
toadstools, any given region of a gill will contain basidia in different stages of development, but in the
ink cap they develop in a definite pattern, with those at the margin of the cap being the most mature,
thus the maturing gills grade from white near the stipe, to pink and through to black at the margin. The
caps therefore dissolve from the perimeter inwards.
Fungi on Decaying Wood

Fallen tree limbs, dead trunks and stumps are valuable habitats for fungi (and in turn for the creatures
that depend on them, such as fungus-eating insects). (See
Deadwood). Brown rots are caused by fungi
that digest the hemi-cellulose and cellulose components of wood, whilst leaving the lignin intact, causing
the wood to darken. White rots decompose all components of the wood, including lignin. Lignin is an
especially tough compound, essentially a complex polymer of phenolic compounds, it is very resilient
physically and chemically and few organism can digest it. The wood has to be moist enough to support
the growth of these fungi.

Fallen limbs, stumps and dead trunks of
beech trees (Fagus) support an especially rich diversity of
fungi. Some of these have a strong preference for beech wood, e.g.
Pholiota adiposa, a large toadstool
with golden-yellow caps and rust-coloured spores, and which also occurs at the bases of living beech
trees. Others are more general, occurring also on the wood of other species, e.g. the sulphur-tuft
(
Hypholoma fasciculare) a medium-sized toadstool of sulphur-yellow (sulfur-yellow) caps. In the final
stages, when the wood is crumbling the puff-ball
Lycoperdon pyriforme can be seen growing on it (it is
unusual for puffballs to grow on wood). A beech stump takes a few years to rot away completely.

Oak (
Quercus) supports fewer fungi, but some are specific to oak. Fistulina hepatica, the beef-steak
fungus, a large bracket which feels and looks like red meat and resembles meat when cut, grows on
living oaks, though it feeds on the dead heartwood. It is a brown rot, darkening the hard wood to a rich
brown colour without destroying the lignin which gives it its structure and such darkened heartwood is
prized by cabinet makers.

Birch wood decomposes especially rapidly, often leaving behind empty cylinders of bark, whilst conifer
wood tends to decompose more slowly, with yew wood persisting for many years.
Fungi on Decaying Leaf Litter

When leaves begin to senesce, whilst still on the tree, they leak materials from their aging cells, which
supports the growth of microscopic 'phylloplane' ('leaf-plane') fungi, particularly
yeasts, including
basidiomycete yeasts (such as
Sporobolomyces) and black yeast, which is part yeast-like, part
mycelial. These fungi initiate decomposition when the leaf falls, but larger fungi, such as toadstools
soon develop and feed on the
leaf-litter (and also bacteria and invertebrates, such as insects, mites
and worms). These toadstools may be general, occurring in a variety of broadleaf and/or coniferous
woods, or they may be more specific, preferring a certain type of leaf-litter. Many toadstools growing
amongst the leaf litter are also mycorrhizae and these are often quite specific, e.g. the fly agaric,
Amanita muscaria, which is found only under birch and pine with which it forms mycorrhizae.

Eventually, only the more indigestible parts of leaves and wood litter and other organic matter remain -
the lignin (from plants), chitin (from animals and fungi) and keratin (from animals) to form
humus.
Oomycetes (water-moulds)        Plasmodial slime moulds        Cellular slime moulds        Lichens        Yeast
Spore-dispersal may be primarily by wind or water, though the role of animals should not be
underestimated.
Wind-dispersed species, such as Mucor plumbeus, the outer surface of the
sporangium is studded with spikes of calcium oxalate, which make the surface water-repellent, keeping it
dry. When ripe, the sporangial wall ruptures and breaks apart, exposing the dry, powdery spore mass
which can be dispersed by air currents. Most species of
Mucor, however, rely primarily on rain-splash to
disperse their spores. In these species, such as
Mucor hiemalis and Mucor ramannianus, the sporangial
wall dissolves, but it does not reveal a dry powdery mass of spores, instead the spore mass expands as it
takes up water, forming a slimy sporangial drop, larger than the original sporangium. The slime dries,
leaving the spores cemented to the columella. These spores cannot be easily blown away by the wind,
but can be scattered by falling rain drops (an example of the use of gravitational potential energy to
disperse spores).
Splash-dispersal of this type is short-range, scattering the spores up to one metre
from the parent sporangium.

Some pin-moulds that rely on rain-splash to disperse the sporangial spores, produce secondary asexual
structures as side-branches branching off the main sporangiophore. Each branch ends in a small
secondary sporangium, or
sporangiole, containing a few spores (4 spores per capsule in Thamnidium
elegans
). These sporangioles are small and very light and detach easily to be blown away by the wind.
Cunninghamella only produces one type of asexual sporangium, called conidia (sing. conidium). These
are interpreted as tiny sporangia, each containing only a single spore. Conidia are borne on single or
branched aerial hyphae called
conidiophores. Conidia easily detach to be blown away.

Each spore inside the sporangium contains one or more nuclei and each may germinate under certain
conditions to form a daughter colony which is genetically identical to that of the parent. Both the parent
and asexually produced daughter colonies are
haploid (that is they contain only one set of
chromosomes).

The mating-type is determined by a single gene with two alleles (versions of a gene), one for plus, the
other for minus. If a plus-type (+) encounters a minus-type (-) then mating and
sexual reproduction
may occur. (Some mycelia may be neutral and these do not mate with either + or - types). When close,
but not touching, the fungi sense the presence of the compatible other and both produce a type of aerial
hyphae, called
zygophores, which arch over towards the neighbouring mycelium. Each mycelium-type
secretes its own
mating hormone and this hormone triggers mycelia of the opposite type to produce
trisporic acid. Two neighbouringh mycelia produce enough
trisporic acid to trigger zygophore synthesis.
Once synthesises, another set of volatile chemical messengers are produced, which diffuse through the
air and stimulate the zygophores to grow towards the colony of opposite type (a process called
zygotropism; tropism being growth in a specific direction triggered by a stimulus). When zygophores of
neighbouring colonies rub against one-another (or at least come in close proximity?) they develop sexual
structures. They often rub together on one side and here they produce lateral swellings, called
progametangia (sing. progametangium). As the progametangia develop, a wall-partition grows, closing
off a multinucleate mass of protoplasm in the end of each progametangium, this multinucleate
compartment being called the gametangium (plural gametangia). Where the neighbouring
plus-gametangium and minus-gametangium meet, their end walls break down and the protoplasts of the
gametangia fuse into a single protoplasmic unit, which is the young zygospore. Plus and minus nuclei
fuse in pairs within the young zygospore which becomes encased in a tough shell or coat when mature
and is now called the
zygospore (or zygosporangium). The zygospore is a resting stage, and after a
period of dormancy it is able to germinate. A hypha emerges which develops into an aerial hypha, a
sporangiophore bearing a spore-capsule at its tip called the germ-sporangium. This ruptures to release
haploid spores which are all either plus or all minus (in some other zygomycetes, spores of both types are
produced).
Above: part of a Mucor mycelium magnified, showing an erect aerial and asexual
sporangiophore bearing a spore-containing spherical sporangium. These sporing structures
give the zygomycetes their common name of pin-moulds. The sporangium is about 100
micrometres in diameter.
mucor
Streaming of protoplasm is readily seen in Zygomycetes such as Phycomyces. The core of protoplasm
in the centre of the hyphae undergoes rapid streaming at 20-40 micrometres per second. This rapid
streaming is similar to the protoplasmic streaming seen in plant cells, but different in origin. In the fungal
hypha it is driven by evaporation (transpiration) of fluid from the growing aerial hyphae - hyphae growing
rapidly upwards to form sporangiophores. It is toward these aerial hyphae that the streaming eventually
terminates, and such streaming presumably helps deliver the materials needed by these rapidly growing
hyphae. In addition, however, there is much slower streaming of the cylinder of protoplasm in the hyphal
periphery, adjacent to the cell membrane and wall. This slower streaming may be in the opposite
direction to the main streaming and is probably driven by the cytoskeleton, as is the streaming in plant
cells. Aerial hyphae initially grow at their tips (apical growth), but then this growth pauses as the
aporangium begins to form and then extension of the hypha continues as it grows beneath the
sporangium (sub-apical growth).

Fungal eyes

Another example of a zygomycete is Pilobolus kleinii which grows as a tiny hairy mould on cow-pats. This
mould produces tiny aerial sporangiophores (each 5 mm or so in height) which bear a terminal swelling,
about 1 mm long, which functions as an eye. On top of the eye is a dark spore mass, inside a black
capsule (sporangial wall) forming the sporangium. Inside the eye is a lens and beneath it, in the adjoining
sporangiophore is a yellow-orange doughnut-shaped ring, which is the light-sensitive retina. The lens
focuses incident sunlight onto one spot on the retina, allowing the fungus to accurately determine the
direction of the light source. (The mould has no brain and the eye does not serve in image formation,
merely as a light-direction sensor). The sporangiophore bends towards the light and when ready the
black sporangium cap and its enclosed spore mass are jettisoned, being fired up to about 2 metres into
the air! This disperses the spores clear of the cow pat, into the grass where they may be eaten by a cow
and pass through to germinate on a fresh cow-pat.
progametangia
gametangia
zygospore
germ-sporangium
Left: two progametangia borne on hyphae of compatible
colonies growing toward one-another. In the case of mucor, the
progametangia are borne on zygophores (aerial hyphae). In
other forms they are simply short upright structures that grow
together like a pincer from mycelial hyphae. In forms capable of
self-fertilisation, the two aerial hyphae are borne on the same
parent hypha.
Gametangia develop where the progametangia meet.
Subsequently the dividing walls between the two
gametangia
break down and the protoplasts of the two gametangia fuse. At
least some of the haploid nuclei fuse in pairs, forming diploid
nuclei.
The fusion cell formed by the fusion of the two gametangia is
the
zygospore, which develops a black and warty outer wall,
which is impregnated with melanin and sporopollenin.
(Sporpollenin is also found in the walls of the pollen grains of
plants). The zygospore wall is very impermeable and resistant.
The zygospore protoplasm is rich in glycogen and lipid food
reserves.
The zygospore is not a dispersive spore, but a resisting spore
and does not germinate immediately. When conditions and/or
timing are right and it does germinate, it gives rise to a germ
tube which develops into an aerial sporangiophore, capped by a
germ-sporangium. The germ-sporangium contains haploid
spores, produced by meiosis. In
Mucor, all the spores in a given
germ-sporangium are of the same mating type (+ or -) though in
some forms they may contain both mating types (or all three if a
neutral type is also formed). This suggests that usually only one
of the 4 haploid nuclei produced by meiosis survives. The
spores of the germ-sporangium are dispersed and germinate to
produce haploid mycelia of a given mating type.
4) Stink horns and cage fungi

These basidiomycetes are varied in shape, but many, such as Phallus, are phallus-shaped. They 'hatch'
from egg-like structures early in the morning and are covered in a sticky fluid which contains the spores
and smells like a rotting corpse. This attracts flies who carry away the sticky fluid and its spores,
dispersing them. By about midday there is no sticky fluid remaining on the stink-horn and it begins to
whither. Stink horns are classified with the gasteromycetes, as although they are not splash-dispersed,
the spores are released by tissue breakdown from a sac-like structure. In some forms, the spore-
producing body expands outwards, from a white egg-like structure, but develops into a lattice-like 'cage'.
These are the so-called 'cage fungi'.

5) Disc and Cup Fungi

The sporocarp is disc or cup-shaped in these ascomycetes. They are usually stalk-less, with the
exception of morels which consist of a wrinkled head on top of a stalk. They generally do not need
stalks, since they shoot their spores a short distance into the air (several millimetres to several
centimetres) just high enough to clear the layer of still air and enter the turbulent layer to be scattered
by the wind. The spores are fired from the upper surface of the disc, or from the inside of the cup. They
have no gills and no visible pores, but are smooth. However, the spore-releasing surface is covered by
microscopic pores. They become hard and brittle when dry, but remain alive, and fell rubbery when
moist. The ascomycete sporocarp (
ascocarp) is called an apothecium when disc or cup-shaped and a
perithecium when flask-shaped.

6) Burnt Fungi

These basidiomycetes also fire their spores into the air, but resemble nodules or raised patches of burnt
and hard wood. They are black, dry and hard to the touch. They grow on rotting wood.

7) Jelly Fungi

Feel like jelly, and are often translucent (like coloured glass). They come in a variety of shapes,
including brain-like masses and ear-like lobes (e.g. Jew's ear fungus). They usually grow on rotten wood.

8) Coral Fungi

Coral fungi, e.g. Clavaria, are basidiomycetes which grow upright, often branching, and so resemble
coral, candle wicks, tiny clubs, candelabras, tiny antlers or tiny flames. The spore-producing surface
covers the end regions of the sporocarp, being exposed as it covers the external surface.

9) Encrusting Fungi

In addition to the burnt fungi, many ascomycetes and basidiomycetes are encrusting, forming velvety
films, cushions or nodules on wood and other surfaces.

10) Truffles

These ascomycetes produce subterranean sporocarps and they belong to the discomycetes, even
though their spore-bearing surface is not open and exposed as in typical disc and cup-fungi. They seem
to rely on animals, such as rodents, finding and eating them in order to disperse them. The most prized
edible truffles belong to the genus
Tuber. The truffles appear to have evolved from typical
discomycetes, and some still have a structure suggestive of a closed cup. The paraphyses form a
convoluted branching network through the ascocarp (a pseudoparenchyma) which contains spherical
asci dotted about, each ascus containing one to four spores only. The asci in truffles do
not rupture to
disperse the spores.

11) Morels

Morels (Morchella) are ascomycetes that consist of a stalk, up to 15 cm tall, bearing a club-shaped
pitted surface, the pits being lined by asci. Like truffles they are prized by humans as food.

12) Rusts and Smuts

The rusts are basidiomycetes of the Uredinales group with over 100 genera and over 5000 species. All
are parasites of plants, being unable to grow in nature without a host (they are obligate parasites). The
smuts or Ustilaginales is another (smaller) group of plant parasites usually classed as basidiomycetes.
Fungal pathogens of plants will be considered in a separate article.

13) Water Moulds and Protofungi

The water moulds and related types, also called the oomycetes are protofungi (in a similar way that
protozoa are proto-animals and algae are protophytes). They produce aquatic spores, called
zoospores, which swim in water by means of flagella. These protofungi are grouped with the protozoa,
slime moulds and algae in the kingdom Protoctista and are no longer classified as fungi by most
biologists.

14) Slime Moulds

These are no longer classified as fungi and are considered a type of protozoan or protofungus and so
included in the Protoctista. There are two chief types:
cellular slime moulds, such as Dictyostelium, and
plasmodial slime moulds like Physarum. They are capable of motility, moving around slowly by crawling.

15) Yeasts

Yeasts are unicellular fungi that produce no sporocarp and typically no hyphae, occuring predominantly
as walled cells which reproduce by budding. Many yeasts are ascomycetes, but some are
basidiomycetes, whilst others have no sexual cycle and produce only asexual spores. Yeasts are
extremely common, accounting in large part for the dusty appearance of fruit like grapes (the yeast
growing on sugars that leak or exude from the grape) and some human infections. Pink films of 'mould'
are often due to yeast. More on
yeast.

More fungi:

  • See also deadwood for fungi that decompose plant remains and biodiversity for more examples of
    fungi.

Bird's nest fungus courtesy of Nicholas Money
Dispersal in bird's nest fungus courtesy of Nicholas Money
Above and below: The bird's nest fungus, e.g Cyathus, Crucibulum. The 'nest' or cup structure is about
1 cm across and the 'eggs'  are the peridiola - the gleba divides into these masses during development
and each peridiolum is encased in a firm wall of interwoven hyphae. Each peridiolum is attached to the
inner cup wall by a hyphal thread called the funiculus. Rain drops striking the cuip scatter off its inner
surface and the larger droplet fragments may carry away a peridiolum up to a meter or so from the
'nest'. The funiculus is sticky and will entangle on any object that it strikes on its projectory. Some of
these fungi, e.g.
Cyathus stercoreus live on herbivore dung, and if the periodiolum comes to rest on
grass it may be eaten by a herbivore and pass out in the dung, in which case the basidiospores will
germinate with a ready-made food source! Other forms grow on rotting wood and sometimes new
colonies are established by the growth of the hyphal case of the peridiolum, without basidiospores
germinating.

Images courtesy of Nicholas Money, Professor of Botany at Miami University. Prof. Money is an expert
on fungal movement and spore dispersal.
polypore fungus
Polyporus squamosus bracket fungi growing on an old sycamore tree in
Fredville Park. This fungus is parasitic but is also found on stumps. This
tree had lost much of its crown but was still very much alive. It is not clear
whether this fungus is growing on the living or dead wood. This fungus is
found most often on beech, elm and sycamore