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Fungi are primarily organisms that cannot synthesise their own food and are dependent on complex organic substances for carbon. Specialized fungi can be pathogenic on the tissues of plants, while others form mutually beneficial relationships with plants and assist in direct nutrient supply to the plants (e.g. mycorrhizal associations).
Many fungi play a very important role in the recycling of important nutrients that would otherwise remain locked up in dead plants and animals. In the decomposition of plant debris, certain fungi are particularly important because of their ability to derive their carbon and energy requirements from the break down of dead and decaying plant cell walls, cellulose and lignin. Fungi are much less dependent on water than other microorganisms, but interactions with other microbes, temperature and nutrient availability will have an effect on their activity. Fungal activity is greatest in decomposing leaves and wood, and tends to diminish in the later stages of decomposition when bacteria become more dominant.
Disease-causing microorganisms have always been inherent members of any living community. In natural ecosystems, characterised by uncontrolled and changeable conditions, their population growth is impeded by the scattered distribution of host plants and, in the case of fungal pathogens, by their dependence on rainfall at the time of spore germination. In managed systems, however, such as agriculture and horticulture, monocultures of crop plant species provide an unconstrained food supply for a pathogen. Irrigated systems also provide a constant supply of water which can enable spores to germinate and cause disease in accessible host plants.
Climatic patterns can affect the types of fungal pathogens that are dominant in a region. For example, low fertility soils favour necrotrophic pathogens over biotrophic pathogens. Necrotrophic pathogens are distinguished from biotrophs because they kill host tissue prior to colonisation. Biotrophic pathogens include powdery mildew, downy mildew, rust, nematodes and viruses. Biotrophs live on living tissue and die when the host plant dies.
The soil conditions that exist at the opening of the cropping season (warm, moist soils and low microbial activity) can favour the growth of a pathogen.
Reduced tillage practices help maintain infested residues at the surface of soil, increasing the damage to young seedlings. Conventional cultivations bury this inoculum source which gets broken-down more rapidly by soil microorganisms than when on the soil surface. Rotations with susceptible hosts can increase the inoculum potential of the pathogen in soil. Certain herbicides also increase the disease severity (e.g. the disease caused by the Take-all fungus and root rot caused by Rhizoctonia).