Soil Fungi
Introduction
Soil is an oligotrophic medium for the growth of fungi. Nutrients for fungal growth are extremely limited for most of the time. Readily available nutrients are present for short periods in a limited zone. For most of the time, fungi are either dormant, or they metabolise and grow very slowly utilising a range of organic molecules. The presence of a living plant dramatically changes the scenario. In general, the concentration of microbes is greatest close to the surface of roots where exudates from the root supply an extraordinarily important source of organic energy to the soil (rhizosphere).
Away from the root, the remains of plants and microbes are the primary source of energy. These remains are digested or oxidised usually very rapidly. Cellulose has a half life of less than 1 month in moist well aerated soil in temperate climates, lignin is usually completely oxidised within 7 months. Modified complex molecules of plant and microbial origin remain mostly in protected anaerobic micro-sites. LINK. The recalcitrant remains are known as humus. Humus consists of a mixture of aromatic compounds that are comparatively resistant to enzymatic degradation: oxidative processes are needed to break the aromatic ring, and fungi are an imortant contributor to oxidation of polyaromatic molecules in soil.
Humus forms an important part of the carbon stored in soil. The loss of humus to the atmosphere because of human activities is an important contribution to the increasing carbon dioxide in the atmosphere. Human degradation of ecosystems may be responsible for some 30% of the existing greenhouse gases, and this carbon comes from soil. If mycologists are to be part of the scientific response to global climate change, efforts to better understand carbon cycling in soil would be a useful place to start.
Lifestyles
The lifestyles adopted by fungi in soil fall into three types: ruderals, mycorrhizal fungi and hyphal forms. LINK 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. The fungi usually sporulate rapidly, and exist through dry periods as asexual spores.
Common genera include Absidia, Alternaria (above), Aspergillus (above), Chaetomium (above), Fusarium, Mortierella, Mucor, and Penicillium (above). These are the fungi that are commonly isolated from soil using soil dilution techniques.
Mycorrhizal fungi subsist almost entirely by tapping into the roots of plants for their organic energy LINK. The fungi are extremely common in soil, though quantification of the fungi is extremely difficult. Up to 5m of living hyphae of arbuscular mycorrhizal fungi can be extracted from 1 g soil. The same quantity of soil may reveal 1,000 colonising 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 LINK. 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 exude simple organic molecules that are a suitable source of carbon for some other microbes, and hyphal remains provide a second nutrient in soil. AM fungi are ubiquitous yet lack clear methods of widespread and rapid dispersal found in ruderals. The life style of mycorrhizal fungi is very different to ruderals.
Finally, a group of fungi exist as hyphae in soil. Spores of these fungi are extremely difficult to find in soil, and some may rarely sporulate. While some of the fungi have the potential to cause disease, it is likely that for much of their lifecycle, these organisms metabolise and grow slowly. They are usually associated with organic fragments, which they slowly degrade. Their isolation from soil requires special techniques LINK. However, once in culture the fungi can grow rapidly utilising a wide range of sources of complex carbon. These fungi exhibit some combative and stress-tolerant characteristics. LINK
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. 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 may also be located within micro-aggregates where it is protected from oxidation. Humus also bonds to various organic pollutants such as polyaromatic hydrocarbons and alanines (and shares a number of similarities) making both unavailable for degradation. Like all polyphenolic complexes, humus readily oxidises when the soil is exposed to oxygen such as following 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 30% 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.
Role of Soil Fungi in Aggregating Soil
We know that development of structure in soil has two components: formation of aggregates and the complementary space between: pores connecting cavities. The pores and cavities hold air and water, the size and connectivity of the spaces determining the quantity of water held, and the rate at which water moves through or is extracted from the soil. Minerals are bound within and attached to the charged surfaces and in solution. The filamentous form of fungi enables enmeshment of soil particles, important in forming aggregates ranging in size from 200 to 2000 µm. However, development of mycelium, especially in artificial culture, and enmeshment are unrelated. Fungi that aggregate soil must attach to the soil particles and the hyphae must remain intact.
Several groups of fungi appear to be involved with aggregating soil. AM fungi are probably the most important soil fungi for soil aggregation. However, the fungi must grow beyond the root surface and intensely explore the soil matrix. Not all AM fungi explore the matrix. In general, species of Glomus and Acaulospora explore beyond the roots, and Gigasporaceae the root surface.
Saprotrophic fungi are probably unimportant for soil aggregation because of the absence of an ongoing source of energy. Given appropriate nutrition, a tiny proportion of saprotrophic Trichocomaceae enmesh soil.
Roots may supply adequate nutrition for endophytic fungi. Root endophytic fungi are currently being tested for their capacity to aggregate soil: even here, a tiny proportion is associated with increased soil aggregation. The mechanism appears to be by enmeshment.
A second mechanism possibly enables formations of micro-aggregates, aggregates less than 250 µm. Extracellular materials released by some fungi increases adherence between particles. A range of fungi express extra-cellular materials but not all materials increase adherence. If these materials attach to surfaces and are deposited within macro-aggregates, with wetting and drying of the soil, may lead to the infill of cavities and closure of pores. Charges on the surfaces will increase attachment. Thus release of extra-cellular materials may have a role in the storage of organic carbon in soil, especially if that material contains recalcitrant materials such as polyaromatic carbon.
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Thus we come to a full circle. Humus is a polyaromatic material that is thought to exist for decades to centuries in soil when it is protected. If fungal extracellular materials contain polyaromatic materials, and they are placed within micro-aggregates where they are protected from oxidation, then they may be the materials that constitute long-lived organic carbon in soil.
Conclusion
Fungi in soil demonstrate a variety of life styles, indicative of the variation in most habitats. Groups of different fungi utilise different carbon resources, with the result that very little organic carbon remains in soil, or passes through the soil in water.
References
Dighton J, White JF & Oudemans P (2005) The Fungal Community (3rd edit). Taylor & Francis.
Dix NJ & Webster J. 1995. Fungal Ecology. Chapman Hall. Ch 7.
Zak JC, in Carroll GC & Wicklow DT 1992 The Fungal Community (2nd edit). Marcel Dekker. Ch 22.
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