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Process of Extracellular Digestion

Introduction

Fungi are heterotrophic organisms. LINK Heterotrophic nutrition means that fungi utilise extracellular sources of organic energy, organic material or organic matter, for their maintenance, growth and reproduction. Energy is derived from the breakdown of the chemical bond between carbon and either carbon or other components of compounds such as a phosphate ion. The extracellular sources of energy may be simple sugars, polypeptides or more complex carbohydrate.

Fungi can only absorb small molecules through their walls. For fungi to gain their energy needs, they find and absorb organic molecules appropriate to their needs, either immediately or following some form of enzymic diminution outside the thallus. The small molecules are then absorbed, used directly or reconstituted (transformed) into organic molecules within the cell.

When you see a skeletonised leaf in the litter, it is because recalcitrant materials remain and digestion is continuing. The fungi that utilise a variety of energy sources usually absorb the simplest compounds first, then the more complex. For instance, the formation of cellulase is repressed by high concentrations of glucose in the cytoplasm. On depletion of primary sources of glucose, enzymes to degrade more complex molecules such as cellulose and starch, are then released. Thus soluble sugars and amino acids are removed first from a leaf released from a tree. Starch is then broken down and absorbed. Subsequently, pectin and cellulose are digested. Finally, waxes are degraded and lignin oxidised. The staggering of energy acquisition results in the efficient utilisation of available energy.

Detection

The regulation of nutrient acquisition appears to be controlled by general phenomena. Only a small group of enzymes, mostly hydrolases, can be detected in the culture filtrate of well fed fungi. This suggests that specific inducers control the manufacture and release of enzymes for degradation. The most common complex carbohydrate available in the environment is cellulose. In the absence of glucose, detection of cellulose, for instance, induces the expression of cellulases. As a consequence, fungi specifically target the breakdown of the cellulose in their environment, and do not waste energy on the unnecessary formation of enzymes for degradation of molecules that may not be present. Fungi have an efficient process to gain energy.

Because of the huge range of potential food sources, fungi have evolved enzymes suitable for the environments in which they are usually found. The range of enzymes, though wide in many species, is not sufficient for survival in all environments. Fungi require other competitive attributes to ensure continued survival. LINK

The opposite is also true. Some fungi have highly specific metabolic capabilities which enable occupation of specific habitats, utilising molecules which are unavailable to other fungi. Further, utilisation of a common and abundant substrate has led many fungi to evolve a range of highly specific degradative enzymes. Among the fungi are species that are generalist in their nutrient requirements, some that have specific nutrient requirements, and many that are in between.

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Excretion of Enzymes

Enzymes are manufactured close to the hyphal tip. Some are packaged in vesicles associated with the Golgi and then delivered to the hyphal tip. The contents are released at the tip. Some enzymes are actively excreted through the plasmamembrane, where they diffuse through or act in the cell wall. LINK Note that the enzymes released from the hyphal tip require an aqueous environment for release and subsequent degradative activity.

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The Enzymes

Fungi excrete a complex array of related enzymes for digestion. The enzymes tend to be present in multiple forms, based on a single genetic sequence, and include a range of isoenzymes, which arise from different genetic sequences. The consequence is that enzyme groups function synergistically to rapidly and completely break down foods. For instance, more than three isoenzymes of cellulase are released by Trichoderma reesei, each of which may be modified post transcription. The enzymes break down different parts of the cellulose polymer, some from the ends of (exocellulase), and others within (endocellulase) the cellulose molecule.

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Digestion of Cellulose

Cellulose is a polymer of glucose which is digested by a variety of enzymes. In simple terms, the enzymes may either cleave glucose dimers from the end of the polymer (exocellulase), or fragment the cellulose polymer into smaller molecules by internal digestion of the polymer (endocellulase). The two types of digestion usually take place simultaneously, though the amount of each enzyme expressed, and the rate of activity differs between fungal species and the environment in which they are functioning. In each case, a glucose dimer is absorbed and this is cleaved within the cytoplasm.

Cellulases are especially common in soil and plant inhabiting fungi. Many fungi in the Ascomycotina and Basidiomycotina are able to digest cellulose. The necessary enzymes are less common in members of the Zygomycotina. Further, cellulases can be extracted from soil. Presence of the enzymes in moist soil may indicate release of glucose dimers available for absorption by all microbes in the near vicinity: indicating a continuing and community-based process of cellulose degradation by microbes.

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Digestion of Lignin

structure of lignin
Structure of Lignin.

Lignin is commonly found in plants: overall, lignin is the second most common organic polymer in the environment. The molecule is long-lived in the environment for two reasons. Lignin is a polymer of phenyl-propanoid units, with a variety of carbon-carbon, and carbon-oxygen linkages resulting in a complex structure. A variety of enzymes are needed to completely degrade lignin. These can be classified into two functional groups: lignin peroxidases and manganese peroxidases. Each species of ligninolytic fungi has its own array of enzymes, and these have different overall oxidative characteristics. Secondly, the enzymes are only induced in the absence of readily available nutrients. Thus degradation of lignin is delayed and may be slow.

Lignin molecules are commonly found associated with cellulose. LINK The lignin may be layered between layers of cellulose, such as in the middle lamellae of wood, or enveloped within or by cellulose. Fungi with ligninases also usually digest cellulose. However, the reverse is not necessarily true. Fungi with cellulases do not necessarily have ligninases. Degradation of lignin is an oxidative process, enabling the fungus to access more cellulose. The nutritional value of lignin to fungi is questionable. Tracer studies indicate that all carbon arising from oxidation of lignin is released as carbon dioxide, and is not taken up by microbes. The ecological importance of lignin oxidation will be explored below.

The fungi with ligninolytic potential are more common in the Basidiomycotina than any other group. Generally, lignin is broken down slowly because the fungi able to degrade the material are uncommon and the environments highly competitive. Even so, most lignin is removed within 7 - 12 months of deposition in arable soil. LINK

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Other Molecules

Different fungi have the capacity to digest a wide variety of complex molecules. Essentially, if the molecule releases energy on digestion then at least one fungus will have enzymes capable of partially or completely digesting the molecule. For example, the kerosene fungus, Amorphotheca resinae is able to colonise the energy-rich preservative creosote. Few other fungi are likely to colonise this substrate providing the fungus with a distinct advantage, though only where creosote and similar materials are present.

The rate of digestion of any one complex substrate may be very slow, and the original molecules may be digested by a suite of fungi acting synergistically. The breakdown products may remain undigested until microbes with appropriate enzymes are activated to digest the compound. The breakdown products may themselves be toxic to some fungi. The processes of fungal digestion of organic matter are complex and variable.

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Absorption of the Products of Digestion

The molecules absorbed through the plasmamembrane tend to be smaller than 5,000 Da, so only simple sugars, amino acids, fatty acids and other small molecules can be taken up following digestion. The molecules are taken up in solution. In some cases, the molecules are processed by enzymes located within the cell wall. For instance, sucrose invertases have been localised in walls of yeasts. Glucose appears to be the sugar preferred by most fungi. Uptake of other sugars is repressed when glucose is available. Similarly, ammonium, glutamine and asparagine regulate the uptake of nitrogen compounds, and cysteine of sulphur compounds.

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References

Dix NJ & Webster J 1995 Fungal Ecology. Chapman Hall. Ch 2

Ingold CT & Hudson HJ 1993 The Biology of Fungi. Chapman Hall. Ch 9

Jennings DH 1995 The Physiology of Fungal Nutrition. CUP. Chs 5,6,7 & 8.

Schwarze FWMR, 2007 Wood decay under the microscope. Fungal Biology Reviews. 21: 133-170.

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Degradation of Lignin

Like cellulose, lignin is an abundant organic polymer found in the environment. Lignin is commonly found with cellulose in wood; 25% of the secondary cell wall of wood may be lignin and lignin may infill gaps in the middle lamella. The oxidation of lignin is especially important because it is commonly closely associated with cellulose, often impregnating wood, protecting the wood from enzymic decay.

Rotten post from side
Rotten post from side.
Rotten post 2
Rotten post from above.
The fungus
The culprit.

 

Degradation of lignin is an oxidative process. The breakdown products are not released into solution and thus available for host uptake. Lignin degradation appears to be a process that releases cellulose. The degradation of wood must involve oxidation of lignin.

Lignin is a complex of branched polymers of coniferyl alcohol, and guaiacyl with syringyl and p-hydroxyphenyl. Lignin varies with source. Major differences exist between monocots, softwoods and hardwoods. Minor differences of composition are found between plant species, leading to specialisation of rotting fungi associated with trees.

Fungi enter wood via the vascular tissues. The elongated structure of vessels and fibres allows vertical penetration, and radially arranged parenchyma rays enable horizontal penetration by hyphae. Adjacent cells of the xylem may be accessed by pit connections. The types of rot commonly described indicate different degrees and types of degradation.

Cubical rot
Cubical rot.
Soft rot
Sloppy soft rot.

1. White rot fungi are thought to completely degrade lignin and cellulose. One, Phanerochaete chrysosporium, has been studied because the lignin degrading enzymes also appear able to degrade serious pollutants such as chlorinated biphenyls. Most white rot fungi are members of Basidiomycota, and a few are Ascomycota.

In different tree species the fungi may either selectively remove lignin before cellulose, or remove both cellulose and lignin simultaneously. The latter is characterised by hyphae forming channels or troughs in the timber as degradation procedes.

2. Brown rot fungi completely degrade cellulose and hemicellulose, and partially degrade lignin. Most are members of the Basidiomycota and include most polypores. The fungi rapidly remove cellulose, and the brittle cubical structure that remains largely consists of the lignin of the outer cell wall and middle lamella. Brown rot is commonly seen in wood from Gymnosperms in the northern hemisphere, and in both Angiosperms and Gymnosperms in the southern hemisphere.

3. Soft rot fungi are unable to completely degrade lignin, and may not completely remove the cellulose from the wood. The surface of the resultant material has a spongy texture. The fungi are commonly Ascomycota.

Fungi are essential for the breakdown of lignin. Only some actinomycetes are able to partially degrade lignin. Thus, degradation of forest debris is entirely reliant on fungi. The fungi commonly degrading lignin are basidiomycota, and the basidiomes found in forests are frequently of species active in lignin oxidation.

 

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Composting

Composting is the microbial degradation of diverse organic wastes in an aerobic thermophilic process resulting in humus. A succession of bacteria and fungi function in three phases of degradation. The process is relatively predictable and is used in mushroom production for forming the growth medium.

The microbial community may be innate or introduced. In any case, the initial stage is where existing epi- and endophytic microbes digest readily available organic nutrients. Rapid removal results in the release of heat which cannot escape from the compost. The temperature increases rapidly to as much as 80 C. The heat kills many of the bacteria and yeasts of the initial stage. Thermophilic and thermotolerant fungi from the compost or the air proliferate through the compost, commencing the degradation of cellulose and hemicelluloses. The degradation of recalcitrant molecules such as lignin and other polyphenolic materials follows, releasing further cellulose in the process. The metabolic rate declines as the rate of degradation declines, and temperature returns to ambient in the third or cooling phase. The microbes are again replaced, this time with air or soil borne species.

The rate of reaction is largely dependent on the moisture and aeration of the compost. While most fresh plant material is largely water, too much added moisture slows the process and causes anaerobic digestion. Too little available moisture and the process slows, because nutrients cannot be solubilised and accessed. Available water is related to both the osmotic potential as well as the total water of the system. The process is also complicated by the release of water from metabolic activity, and the losses through evaporation from the surface.

Composting also requires oxygen and nitrogen. In the absence of oxygen, silage will form due to the presence of lactobacilli. Adequate nitrogen is also essential. Low proportions of N, above a ratio of C:N of about 12 - 15, will slow the rate of degradation during the early stages of compost formation. The latter stages are less affected as many lignin-degrading fungi have the capacity to autolyse and recycle N within the mycelium. Phosphorus and Calcium concentrations are also important.

During the active period of composting the pH rises to about 8 to 8.5 because of the release of ammonia. Many of the materials composted contain significant protein, which is converted to ammonia, mopping up protons in the process. The pH determines the status of the ammonia. At high pH, it is present largely as ammonia which may evaporate, and at low pH as ammonium which remains in solution. This is important, as ammonia is toxic to many organisms. However, compost for mushroom farming requires ammonia formation as the ammonia forms stable N complexes with organic matter by reacting with sugars, phenols etc. Normally, the concentration of ammonia drops as the compost forms. The pH also drops as protons are released, eventually reaching around 6.5.

Initially, compost is a nutrient-rich medium. Microbes compete fiercely and the available energy declines. LINK Many potential pathogens (plant and animal) are destroyed at this stage because they are poor competitors and intolerant of heat. Most seeds are also killed by the heat. The compost passes through several stages in which the plant materials become increasingly unidentifiable. The final product is a friable complex of organic polyaromatic materials called humus. Humus consists of materials such as polymerised aromatic compounds, lignin and wax derivatives, and molecules derived from other complex compounds of plant and microbial origin. An important molecule from fungi is thought to be melanin, both the expressed and wall-bound forms. Products of melanin breakdown may also be an important component of humus.

Composting is analagous to the breakdown of litter in the environment, though composting is much faster. One resultant material is humus, and the compost is of considerable importance for the function of soil and the growth of plants.

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Fairy Rings

The fungal community under pastures and lawns is complex and not well understood. We might expect to find arbuscular mycorrhizas in the roots of most plants, and hyphae of AM fungi would be common in the soil phase. LINK The plants would host a variety of endophytes and plant pathogens. Also present would be a variety of saprotrophic fungi degrading the litter. Included among the saprotrophs are those that form fairy rings.

Fairy rings are dark circles of grass which in autumn contain fruiting bodies of one of a variety of basidiomycetous fungi. They are usually agarics though occasionally puff balls also form a fairy ring. The ring is the result of the establishment of the fungi in a relatively uniform soil. The mycelium grows outwards from the point of establishment in the upper layers of soil. The fungi grow on plant roots and litter that are incorporated in the soil. Only the outer edge radiating from the centre is alive. Behind the outer edge, the mycelium dies. Degradative digestion of plant material releases minerals which fertilise the grasses. As a result, the fruiting bodies appear among lush plant growth in autumn. Inside the ring, grasss grows less vigorously because of reduced mineral availability, and because the fungi release hydrophobic molecules that make the soil water repellent. Fairy rings may be many years old, and their regular appearance is the basis of many folk tales.

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