Soil Fungi: Distribution, Life Style and Benefits | Soil Science

In this article we will discuss about:- 1. Distribution of Soil Fungi 2. Lifestyles of Soil Fungi 3. Common Genera of Soil Fungi 4. Benefits of Soil Fungi 5. Fungal Associations.

Contents:

1. Distribution of Soil Fungi
2. Lifestyles of Soil Fungi
3. Common Genera of Soil Fungi
4. Benefits of Soil Fungi 
5. Fungal Associations

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1. Distribution of Soil Fungi:

Fungi are found wherever there is hard, carbon-rich woody organic matter. This could be dead rotting trees in a forest, leaf litter on the surface of orchard soils, or plant roots.

Mycorrhizal fungi are found naturally in all soils. Techniques to determine their presence usually focus on indirect methods or look at the colonization of plant roots and are therefore not that reliable. It is difficult to get mycorrhizal fungi to grow outside their natural state, but staining techniques and microscopy have been useful in identifying mycorrhiza from soil and plant samples.

Fungi tend to dominate over bacteria and actinomycetes in acid soils as they can tolerate a wide pH range. Fungi can survive in the soil for long periods even through periods of water deficit by living in dead plant roots and/or as spores or fragments of hyphae.

A gram of garden soil can contain around one million fungi, such as yeasts and moulds. Fungi have no chlorophyll, and are not able to photosynthesis; besides, they can’t use atmospheric carbon dioxide as a source of carbon, therefore they are chemo-heterotrophic, meaning that, like animals, they require a chemical source of energy rather than being able to use light as an energy source, as well as organic substrates to get carbon for growth and development.

Many fungi are parasitic, often causing disease to their living host plant, although some have beneficial relationships with living plants. In terms of soil and humus creation, the most important fungi tend to be saprotrophic, that is, they live on dead or decaying organic matter, thus breaking it down and converting it to forms which are available to the higher plants. A succession of fungi species will colonize the dead matter, beginning with those that use sugars and starches, which are succeeded by those that are able to break down cellulose and lignins.

Fungi spread underground by sending long thin threads known as mycelium throughout the soil; these threads can be observed throughout many soils and compost heaps. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g., mushrooms, toadstools and puffballs) which may contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to lie dormant for up to years until the right conditions for their activation arise or the right food is made available.

The range of fungi known to occur in soil is very wide, from chytrids to agarics, from saprophytes to root parasites, from parasites of amoebae to parasites of man. Interest in fungi occurring in soil has been great and considers that soil has probably been studied more extensively than any other natural habitat of fungi.

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2. Lifestyles of Soil Fungi:

The lifestyles adopted by fungi in soil fall into two types:

i. Ruderals,

ii. Mycorrhizal fungi

i. Ruderals:

Ruderals take advantage of the flushes of nutrients usually associated with rainfall. The water moving through soil carries with it dissolved organic molecules flushed from plant surfaces, surface litter and dead microbes. The fungi respond immediately, and grow actively while soil remains moist.

Members of the order Mucorales are widely considered to be ruderals. The genera Mucor and Rhizopus are common in soil and air, and Pilobolus and Pilaira on dung. Their sporangiospores germinate rapidly in response to available energy. The mycelium develops rapidly when nutrients are available. Sporangiospores or other reproductive propagules are formed very soon after initiation of the mycelium. At the first sign of depletion of nutrients, or competition, the mycelium starts to collapse. Each individual is “alive” for a short time.

Ruderals capture the readily available resources quickly. However, they appear unable to utilize complex carbohydrates because they lack the appropriate array or activity of enzymes. Energy is rapidly transformed into reproductive units, not hyphae. Sporangiospores appear to have a relatively short life, thus the fungi do not survive for long or at high densities in stable, low nutrient, highly competitive habitats.

These fungi usually sporulate rapidly, and exist through dry periods as asexual spores. Common genera include Absidia, Aspergillus, Chaetomium, Fusarium, Mortierella, Mucor, and Penicillium. These are the fungi that are commonly isolated from soil using soil dilution techniques.

ii. Mycorrhizal Fungi:

Mycorrhizal fungi subsist almost entirely by tapping into the roots of plants for their organic energy. The fungi are extremely common in soil, though quantification of the fungi is extremely difficult. Up to 5 m of living hyphae of arbuscular mycorrhizal fungi can be extracted from 1 g soil. The same quantity of soil may reveal 1,000 colonizing propagules of the same fungi, and maybe the same number of spores of ruderals. As ruderals are defined as organisms that form huge numbers of survival units, one might argue that mycorrhizal fungi in these soils should be classified as ruderals.

The lifestyle of mycorrhizal fungi is however, much more stable. While ever the host is alive, the fungi have access to organic carbon, and their proliferation is comparatively measured. Indeed, they probably exude simple organic molecules that are a suitable source of carbon for some other microbes. AM fungi are ubiquitous yet lack clear methods of widespread dispersal found in ruderals. The life style is very different.

Finally, a group of fungi exist as hyphae in soil. Spores of these fungi are extremely difficult to find in soil, and some- may never sporulate. While some of the fungi have the potential to cause disease, it is likely that for much of their lifecycle, these organisms metabolize and grow slowly.

They are usually associated with organic fragments, which they slowly degrade. Their isolation from soil requires special techniques. However, once in culture the fungi can grow rapidly utilizing a wide range of sources of complex carbon. These fungi exhibit some characteristics of combative and stress tolerant fungi.

Fungi do not appear to readily degrade all forms of complex organic carbon. Humus is the name given to the complex of organic materials that may be resident in soil for decades to centuries. Humus consists of a suite of mixed polymers of aromatic and aliphatic compounds, largely derived from lignin (plant) and melanin (all organisms including fungi). Some 60% of organic carbon in soil may be humus.

Humus is resistant to degradation because it covalently bonds the reaction sites to metals and clay minerals making the sites unavailable to enzymic attachment. Humus also bonds to various organic pollutants such as polyaromatic hydrocarbons and alanines (and shares a number of similarities) making both unavailable for degradation.

Further, humus is often trapped within soil aggregates and therefore has an exposed diameter that effectively prevents bacteria from accessing the complex. Humus breaks down more readily when the soil is exposed to oxygen such as by cultivation, when soil is acidic and when the moisture level is around 20%.

The fungi play an important role in soil, degrading complex sources of organic carbon, some of which may be organic pollutants. While degradation is part of the normal cycle of carbon and other elements, loss of carbon from soil, especially agricultural soil, is responsible for as much as 20% of the increased CO₂ in air, contributing to global heating. Indeed, a reduction of fungal degradation of organic carbon leading to an increase of humus in soil may be one mechanism whereby both improved soil quality and carbon sequestration may be achieved.

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3. Common Genera of Soil Fungi:

Both the generic composition and the size of the flora vary with the type of soil and with its physical and chemical characteristics. Most species are mesophilic in their temperature relationships; however, a few thermophilic strains can be demonstrated in normal soil, during heating of rotting composts.

Among the terrestrial thermophiles are species of Aspergillus, Humicola, Mucor, Chaetomium etc. The dominance of one or the other group is frequently related to factors like season, vegetative cover, type of soil, application of inorganic fertilizers etc.

Some of the important procedures for studying soil fungi are as follows:

1. Rossi-Cholodny buried slide procedure

2. Florescent microscopy, and

3. Conventional plate count.

Most isolates are placed in one of the two classes, Hyphomycetes or Zygomycetes. The list of classes is derived from the scheme of classification proposed by Answorth.

1. Hyphomycetes:

Lack of sexual stages. Form a mycelium that has spores on special branches (the sporophores) or that bears no spores. Examples: Aspergillus, Botryotrichum, Botrytis, Cladosporium, Curvularia, Cylindrocarpon, Epicoccum, Fusarium, Fusidium, Geotrichum, Gliocladium, Myrothecium, Paecilomyces, Penicillium, Rhizoctonia, Scopulariopsis, Stachybotrys, Stemphylium, Trichoderma, Trichothecium, Verticillium.

2. Coelomycetes:

Lack of sexual stages. Spores in pycnidia. Examples: Coniothyrium, Phoma.

3. Zygomycetes:

The sexual resting spores are zygospores. Examples: Absidia, Cunninghamella, Mortierella, Mucor, Rhizopus, Zygorhynchus.

4. Pyrenomycetes:

Spores in the sexual stage are ascospores. Examples: Chaetomium, Thielavia.

5. Oomycetes:

Possess biflagilate motile cells known as zoospores. Spores in the sexual state are oospores. Example: Pythium.

6. Chtridiomycetes:

Uniflagilate spores and produce oospores. Commonly called chytrids.

7. Hymenomycetes:

Sexual spores are basidiospores. Commonly called basidiomycetes.

8. Acrasiomycetes:

Have a free-living amebal phase, the abebae combining to dorm a pseudoplasmodium.

9. Hymenomycetes:

Sexual spores are basidiospores. Commonly called basidiomycetes.

10. Acrasiomycetes:

Have a free-living amebal phase, the abebae combining to dorm a pseudoplasmodium.

The term yeast has no taxonomic validity, but the group includes fungi that exist primarily as unicellular organisms that reproduce by budding or fission. The genera of soil yeasts most frequently isolated are Candida, Cryptococcus, Debaryemyces, Hansenula, Lipomyces, Pichia, Pullularia, Rhodotorula, Saccharomyces, Schizoblastosporium, Sporobolomyces, Torula, Torulaspora, Torulopsis, Tricjosporan and Zygosacchatomyces.

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4. Benefits of Soil Fungi:

Fungi perform important functions within the soil in relation to nutrient cycling, disease suppression and water dynamics, all of which help plants become healthier and more vigorous.

1. Decompose Woody Organic Matter:

Along with bacteria, fungi are important decomposers of hard to digest organic matter. They use nitrogen in the soil to decompose woody carbon rich residues low in nitrogen and convert the nutrients in the residues to forms that are more accessible for other organisms.

Increase Nutrient Uptake:

Mycorrhizal fungi are well known for their role in assisting plants in the uptake of phosphorus. Phosphorous (P) is not mobile in the soil and having a good level of mycorrhizae can improve the P nutrition of the crop. Mycorrhizae is the most efficient mechanism for P uptake, especially under stress conditions. Nitrogen, iron, copper, zinc, and water uptake is also improved by mycorrhizal fungi.

In recent years, it has been found that mycorrhizae produce glomalin (a protein) which improves soil structural stability. In addition to greater uptake of P and other nutrients, mycorrhizae improve water use efficiency, increase plant vigor, decrease plant root pathogens, and can decrease the susceptibility to nematodes.

Ectomycorrhizal fungi can benefit plants by promoting root branching and increasing nitrogen, phosphorus and water uptake due to their large surface area and internal cellular mechanisms.

2. Improve Plant Resilience:

The sheer size and mass of fungal hyphae help decrease plant susceptibility to pests, diseases and drought.

3. Improve Soil Structure:

Fungal hyphae bind the soil particles together to create water-stable aggregates which in turn create the pore spaces in the soil that enhance water retention and drainage.

4. Provide a Hospitable Environment:

To ensure fungi remain in the earth the soil environment must be kept as hospitable as possible. This means there must be enough food (organic matter), suitable host plants (if necessary), water and minimal disturbance of the soil.

5. Reduce Tillage:

Tillage has a disastrous effect on fungi as it physically severs the hyphae and breaks up the mycelium.

6. Reduce Fungicide Use:

Broad-spectrum fungicides are toxic to a range of fungi. Their use will result in a decline in the numbers of beneficial types. Herbicides are not generally thought to affect fungi directly, though the removal of some plant types may affect the distribution of different fungi types.

7. Grow Plants that Encourage Mycorrhizal Fungi:

There are certain plant groups that do not form associations with mycorrhizal fungi. When these plants are included in a rotation, fungi numbers drop due to the lack of host plants and this reduces fungi colonization.

A bare fallow has the same effect. Mycorrhiza increase under pasture because pasture includes highly mycorrhizal plants such as grasses and legumes. VAM numbers reduce under wheat, canola and lupine. A low level of mycorrhizal colonization in plants is also associated with high available phosphorus levels in the soil.

To enhance beneficial fungi in the soil consider the following practices:

1. Reduce tillage to avoid disruption of hyphae networks.

2. Reduce fertilizer inputs (especially phosphorous) to encourage nutrient scavenging by fungi.

3. Increase the number of crops in the rotation.

4. Plant cover crops to maintain the presence of living roots as hosts.

5. Use bio-control measures for weeds and pests to reduce the impact of fungicides and other pesticides.

Fungi that colonize the root zones of plants and surrounding soil can be beneficial for plant growth. As the fungi enlarge and weave through the root zones, they send threads, far from the roots, to colonize the soil and produce water stable aggregates that link up as macro-aggregates.

This maximizes the percolation of moisture and air into the root zones, improves soil structure and promotes subsurface plant growth. Once colonization has occurred, the fungi suck up nutrients that, in effect, improve the nutritional status of the plant and boost its ability to resist stresses from drought and disease, as well as pests.

Seed Inoculation:

Inoculating seed with beneficial microbes, prior to planting, promotes the establishment of fungi in the root zone. The benefits associated with this process include enhanced rooting and soil stabilization, reduced shock, and the establishment of symbiotic relationships with the plant and other beneficial microbes including nitrogen fixing microbes and phosphate solubilizing microbes that can dissolve phosphorus and make it available for plant uptake.

When seed inoculation is not possible, beneficial microbes can be applied after planting. For example, in established orchards, vineyards, plantations etc. where seed inoculation is impossible, beneficial microbial combinations, including fungi, can be injected into the root zones.

Fungi do however have limitations, including variations in plant response and the correct species of fungi must be used.

It is however important to understand that the use of synthetic chemicals and pesticides can adversely affect the soil microbial balance and cause the benefits associated with fungi and other microbes to be lost. Tillage, that disturbs the plant roots, can also have an adverse effect on soil fungi.

This is partly because of the importance of fungi as plant pathogens, partly because of their importance in the decomposition of plant and animal residues, and partly through interest in mycorrhiza and the rhizosphere.

Those fungi that are able to live symbiotically with living plants, creating a relationship that is beneficial to both, are known as Mycorrhizae (from myco meaning fungal and rhiza meaning root). Plant root hairs are invaded by the mycelia of the mycorrhiza, which lives partly in the soil and partly in the root, and may either cover the length of the root hair as a sheath or be concentrated around its tip.

The mycorrhiza obtains the carbohydrates that it requires from the root, in return providing the plant with nutrients including nitrogen and moisture. Later the plant roots will also absorb the mycelium into its own tissues.

Much of the work on fungal floras of the soil has been essentially floristic, but more recently there has been emphasis on the ecology of fungi in soil, on the habitats of individual species and the parts they play in the biochemical processes that take place in soil. One of the organisms consists mainly of resting structures in a mosaic of micro- habitats.

They often make little mycelial growth but bursting into activity when some event brings fresh nutrient to resting cells which can exploit it. Root growth, litter accumulation and the activity of the soil fauna play important parts in producing such events. Further, so little is known about some fungi in soil that we cannot be sure that we are not looking at merely half of the picture.

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5. Fungal Associations:

Lichens:

Lichens are often described as if they were a species. However, this is not correct. They are a unique symbiotic association of two very different species- an alga and a fungus together forming what looks like a new type of organism. They are not capable of sexual reproduction to produce other lichens.

They can only reproduce asexually by producing soredia, a fragment containing both the alga and fungus. Despite this, some 20,000 “species” of lichens have been described but they can be placed in no kingdom, Calling different types of lichens species is like calling a termite with its symbiotic Trichonympha (protists) a single new species. They are obligate associations, not new types of organisms.