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The processes used by fungi to grow have far-reaching
consequences. It is fair to say that without fungi, the whole world
would grind to a halt!
1. Decomposers
2. Symbiosis
1. The Decomposers
Decomposition may not seem very important at first
glance, but without fungi and other decomposers (such as bacteria)
we would be walking neck-deep in dead plants and animals! In fact,
we would not exist at all, as all the nutrients required to feed
us would be locked up in the dead organisms.
a) – How the world works…
If
we consider the ways in which all living things obtain their
energy to grow and reproduce, we can begin to appreciate the
importance of decomposers.
Energy flows from the Sun to
the Earth... |
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This energy is absorbed by green plants
which use it to photosynthesise new carbon
compounds from carbon dioxide in the atmosphere.
These new carbon-based (organic) compounds
are then used to build new plant material, and to feed existing
plant material with high-energy sugars.
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The new plant material or Net Primary Production
(NPP) can then be eaten by herbivores.
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These in turn are eaten by
carnivores, which may be eaten by yet more
carnivores... but the energy is still ultimately derived from
plants and from the sun. |
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is used make new animal material, but most of the energy is
used to maintain existing cells in the animal, and (in the case
of warm-blooded animals such as mammals and birds) to keep it
warm. |
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Very little energy is available to be passed on to the animal
that eats the herbivore, so it will need to eat a lot of herbivores
to make up for the energy lost by the effort of catching the
herbivores.
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This process of Bigger Things
eating Smaller Things goes on until the point at which it
becomes impossible for a Bigger Thing to eat enough Smaller
Things to gain enough energy to live.
This is, of course, a huge over-simplification... but for
our purpose, it should do. |
© Seran Dolma (and all similar
illustrations on this page)
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So far, we have seen that the flow of energy is in one way, with
energy being transferred in one long, but relatively straight chain,
and energy being lost at each point, as heat, waste products and
general wastefulness. At first glance, this seems to be entirely
sustainable as long as the nuclear processes happening
in the Sun keep on happening. However, light energy alone from the
Sun isn’t enough to keep this food chain operating! Two other
things are needed, atmospheric carbon
and inorganic nutrients.
Given that carbon dioxide (CO2)
makes up over 0.03 % of our atmosphere, by volume, and that CO2
levels are increasing at the moment, then you might think that availability
of atmospheric carbon could never be a problem. But present levels
of CO2 are nothing compared to the
levels present billions of years ago, before algae and cyanobacteria
started the game of photosynthesis. Decomposers play a vital role
in recycling carbon, and also in recycling inorganic nutrients so
that they become available to be used again rather than staying
locked up in plant and animal tissue. Without decomposers, the pool
of such nutrients present in soils, the atmosphere, seas and rocks
would not last for long.
b) The Decomposer Subsystem
In almost all terrestrial environments, decomposers
are active, quietly degrading the Dead Organic Material
(or DOM) produced either as waste products or as the result
of organisms dying. This is a great amount, with the contribution
from plants alone exceeding 75 % of the NPP! The processes outlined
here are happening this very moment, in a patch of soil near you!
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Most DOM is in the form of dead
plants and leaves. Let’s follow the journey of the molecules
found in a single oak leaf through a forest decomposer subsystem.... |
| Deciduous leaves are shed at the
end of every growing season by a process known as abscission.
We don’t need to concern ourselves with what abscission
actually means, but suffice to say that our leaf is chopped
off the tree, and is filled with dead cells that contain proteins,
nucleic acids, carbohydrates, lipids and all the chemicals needed
(in theory) to form a new leaf. But life is not simply a case
of throwing together different chemicals in a nicely defined
formula, and in their current state the molecules in the leaf
are of no use at all to the oak tree or to any other plant. |
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As the leaf hits the forest floor, it is abundantly
clear that the processes required to maintain the leaf in working
order are no longer going on. A certain amount of spontaneous damage
occurs, due to residual enzyme activity. Water within the leaf can
no longer be managed, and structural damage occurs. The dead leaf
has simply lost the lifelong battle against the Second Law of Thermodynamics,
and is going towards random disorder. Sooner or later, though, soil
animals are bound to come along and decide to eat the leaf,
and to extract some energy from it.
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Let’s say that an earthworm
eats the leaf. Of greater interest to us than the energy and
nutrients obtained by the earthworm, is the fact that an earthworm
will chew up an average oak leaf to give about 1 billion fragments.
This is the key effect of soil animals: disrupting the DOM.
Despite the sometimes enormous numbers of soil animals present
– nematode worms can be present at up to 120 million worms
per square metre – the effect that they have is quite
small, contributing less than 10 % of the entire process of
breaking down our oak leaf. |
The chewing-up action, or comminution,
provides a much greater surface area for attack by microbes. The
highly fragmented leaf can then be fed upon with much more efficiency
than before. Soil bacteria play a role in this digestion, but the
key players are the fungi. Fungi have a tremendous
biochemical toolkit in the form of a great number of extracellular
enzymes that can digest a wide variety of substrates, even complex
polysaccharides like lignin. Fungi can grow towards nutrient sources
and force their hyphae
into solid substrates. Therefore, fungi can take advantage of any
nutrient source presented.
By now, the polymers of which the cells were made
are rapidly fading away to give monomers. DNA molecules will have
been broken down to give nucleotides, and proteins will give amino
acids. In the monomer form, materials can be used to biosynthesise
new polymers and provide energy by the means of catabolism
to create ATP which is the energy currency of the
cell. This is done by the fermentation and subsequent
oxidation of chemical bonds to release chemical
energy. When we consider decomposition, we are mainly interested
in the end-products, rather than how this has occurred. The endpoint
of catabolism sees carbon oxidised to the extreme, with the maximum
number of oxygen atoms attached – CO2.
This diffuses into the atmosphere, and can be used for photosynthesis
at some point in the future. At this point, we need to remember
that while the bulk of the oak leaf was made up of carbon, hydrogen
and oxygen, the cells also contained nitrogen and phosphorous in
DNA and proteins, and ions were found freely within the cell, attached
to proteins, or acting as enzyme cofactors. These too are important
in the decomposer subsystem, and are released as ions into the surrounding
environment.
The evidence of such decomposition is plain to
see around us, as the soil is essentially decomposition in progress,
containing DOM that is being broken down, and releasing CO2
and nutrients to be used by plants as their NPP. Environmental Mycologists
can track the fate of atoms through ecosystems using molecules labelled
with rare isotope atoms, and then picking up their signal using
an expensive bit of kit known as an isotopic ratio mass
spectrometer. If we were rather whimsical about the processes
involved, and decided our oak leaf fell to the ground close to the
roots of the same oak tree, then it’s possible that one day,
the molecules of that oak leaf will find their way into a new oak
leaf!
c) The special challenge
of wood
As any botanist will tell you, wood is plant tissue
that has undergone secondary thickening with a polysaccharide
called lignin. The subunits of this polysaccharide
are joined by a variety of chemical bonds at a number of different
angles; this is called a branched polymer. This
makes breaking lignin down very difficult. It may help to think
of a branched polymer as a tree that needs to be cut down. To cut
down a tree, a person would start by using a chainsaw (digestive
enzymes…) to cut the tree into more manageable pieces, usually
at the base of the branches. Now imagine in any given tree how many
different angles, and thicknesses of branches, you’d have
to cut through. It’s the same with lignin. Whereas the subunits
of linear polymers such as cellulose are all joined
by a single type of bond (the beta-1,4 glycoside bond in the case
of cellulose), which makes it easy to digest the chain with a one-size-cuts-all
enzyme such as cellulase, lignin needs a number
of different enzymes (ligninases) to break it down.
In wood, cellulose, lignin and
a third polysaccharide, hemicellulose are found
together in a material called lignocellulose.
The ratio of carbon atoms to nitrogen atoms in
wood exceeds 200:1, meaning that very little nitrogen is available
for use in making new tissue, so wood is a very poor nutrient source.
Combined with the strong, densely packed lignin fibres, wood makes
for very poor eating. It stands to reason, then, that wood is the
slowest DOM to decompose and only very resourceful organisms decompose
it.
Three main kinds of fungi have adapted to make
use of this resource, the Soft Rot fungi, the Brown
Rot fungi and the White Rot fungi, but
only the white rot fungi can handle lignin.
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Soft Rot fungi
These include the Trichoderma fungi, and only attack
the cellulose component of dead wood, as they are only “equipped”
with cellulase enzymes. The main mechanism they use to get
past the tightly packed lignin fibres is to swell them with
water.
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Brown Rot fungi
These fungi use cellulase and hemicellulase enzymes to attack
wood. Again, however, lignin is just too unpalatable for them
to be able to digest. Brown rots also use the power of oxidation
with hydrogen peroxide to attack the cellulose
as it diffuses through the wood.
© Gareth W. Griffith
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One type
of brown rot fungi, dry rot (Serpula
lacrymans; left) can do this to even dry wood by
translocating water from one wet area
to a dry area! As such, dry rot fungi pose major structural
hazards. |
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White
Rot fungi
These fungi digest where other fungi just can’t
reach; Their biochemical toolkit is significantly enhanced
by having ligninases which can tackle
lignin effectively, leaving the wood white in appearance,
hence the name. A good example of a white rotter is
Coriolus versicolor. |
© J. Day |
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| Due to their different abilities as wood decomposers,
these three types of fungi can be seen to occupy different niches,
even on one piece of wood! |
Zone lines between white and brown
rots growing in a beech trunk.
© Gareth W. Griffith |
2. Symbiosis
While a great many fungi are happy to go it alone,
fungi can often exist in partnership with another organism; we shall
consider three such non-pathogenic biotrophic interactions:
a) Mycorrhizas
About 75 % of all plant species have mycorrhizal
interactions with fungi. Mycorrhizas are close associations between
plant roots and soil fungi, and are of three kinds, each allowing
net transfer of certain nutrients to the plant. Mycorrhizas can
be thought of as “roots by proxy”! In some cases, up
to 30 % of the root weight can be fungal in origin. Such systems
are far more successful in getting nutrients, due to the number
of exoenzymes that can be brought to bear by fungi. The three kinds
are:
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Sheathing Ectomycorrhizas
These occur on tree roots,
and exist in a structure called the Hartig net.
They rely on direct contact with the plant roots to allow
the transfer of nutrients between the fungus and roots.
The fungus exchanges both nitrogen and phosphorus with
the plant. Usually, only fungi of the phylum Basidiomycota
engage in this sort of ectomycorrhiza, with Amanita
muscaria, the infamous fly agaric fungus (pictured
right), being one fungus that is part of a sheathing ectomycorrhiza.
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| Vesicular
– Arbuscular Mycorrhizas
Can be abbreviated VAMs to avoid
tongue twisting. VAMs are formed by Zygomycetes
such as Gigaspora in order to exchange phosphates
by intracellular structures known as vesicles
and haustoria-like
arbuscules. Such VAMs are usually obligate
and very ancient.
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Ericoid Mycorrhizas
These are formed on peaty soils and form associations
with shrubs like heather by growing around the roots and forcing
in coils of hyphae. The fungi in such mycorrhizas are usually
ascomycetes
such as Hymenoscyphus, and they exchange nitrogen. |
b) Lichens
Symbioses between fungi and
photosynthetic algae and cyanobacteria
form symbionts called lichen
with nutrient transfer being unidirectional, to the
fungus. Over 20 % of all known fungi, usually ascomycetes
(over 30,000 species) are in symbiosis with lichen, but only
a handful of algae and cyanobacteria are involved with fungi,
and the photosynthesis-derived carbohydrate transferred from
the algae or cyanobacterium depends on the species itself
– for example Trebouxia gives fungi ribitol,
whereas Trentepohlia gives fungi erythritol. Both
carbohydrates are polyalcohols. Cyanobacteria, however, transfer
sugars such as glucose to the fungus.
In all cases, fungi appear to be the ones
benefiting most from this symbiosis. If a lichen colony is
split in the laboratory into the constituent organisms, then
in most cases the algal or cyanobacterial species (the photobiont)
is likely to thrive in pure culture, whilst the fungal partner
(the mycobiont) is likely either to die or
to change its biology significantly |
© J. Day |
c) Symbioses between animals and fungi
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Termites
One of the more unlikely symbioses and perhaps the most spectacular
is that of the old world termite Macrotermes and a
basidiomycete
fungus, Termitomyces, a member of the agaric family.
Termites seem to be the only non-human biotechnologists, as
the termite nest is an extremely
good fermentor. The termites carry Streptomyces bacteria,
which live as part of the termite’s natural flora
and excretes antibacterial substances. This reduces competition
between the fungus and other microbes. The termites chew up
cellulose-rich
material, but they lack the enzymic toolkit to be able to digest
their food. All their chewing does is serve the fungus, by increasing
the surface area for attack by fungal exoenzymes.
The fungus itself is large, and can weigh over two and a half
kilograms. Termitomyces lives in the termite nest,
which provides the ideal conditions for its growth. The nest
is aligned along the north-south line, so that it is warmed
by the early morning sun and evening sun but recieves little
direct sunlight when the sun is strongest at midday. The nest
also has vents, which allow convectional cooling by cool air
currents. As the termites return to the nest they deposit their
faeces on the fungus, which breaks down the cellulose
and hemicellulose. The termites eat parts of
the fungus, and the fungal enzymes continue to decompose the
plant material while in the termites’ guts. As a result,
the termites get their food in a digestible form, and the fungus
gets fed and sheltered. This mutualistic interaction
makes termites the most successful agents of decomposition in
the tropics. Up to 25 % of the available biomass
in East African grasslands goes down the termite pathway!
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Rumen
Mycology
Cows, as we know, have more than one stomach. These “stomachs”
are adaptations to allow them to gain as much nutrition
as possible from plants. However, most of the hard work
is done by microbes in the rumen, one
of the stomachs. Very high concentrations of microbes
are present, with up to 1011
microbial cells per gram! The types of microbes involved
include a great number of different bacterial and protozoal
species, but abount 8%, by weight, are fungi. Most of
these are members of the chytridomycota
and are adapted to life under anaerobic
conditions. As with termites, the cow benefits from the
digestable products of fungal exoenzymes,
and the fungi get fed as well. |
Cyllamyces aberensis
- an example of an
anaerobic gut fungus (chytrid)
© Emin Ozkose et al. |
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