Soil fungi: diversity and detection

The great majority of the 80 000+ fungal species so far named and described are likely to occur in the soil environment at some stage in their life-cycle. Fungi therefore have many different functions in soils, which include both active roles, such as the degradation of dead plant material, or inactive roles where propagules are present in the soil as resting states. Current knowledge of fungal diversity in soil is based largely on observations of fruiting bodies present in an environment, or from cultures obtained from soil isolation exercises. Both of these approaches have serious limitations for the detection of the true diversity in any chosen environment. An organism that exists only in a mycelial form in the soil is unlikely to be identified from direct observation if a fruiting body is not formed. Therefore, classical observation through direct microscopy will give a greatly reduced measure of the true diversity in the environment. Culturing fungi from soil isolations will only result in the detection of those propagules that are able to grow and sporulate on the isolation medium used. This again will lead to a greatly reduced measure of diversity, as at the present time only about 17% of the known fungal species can be successfully grown in culture. The recovery of a culture from soil also does not distinguish whether the fungus was an active part of the original ecosystem or present in an inactive resting state. The development of molecular techniques has provided a new range of tools that can provide clear insights into specific interactions and activities in soil environments. The combination of broad spectrum polymerase chain reaction (PCR) detection, coupled with single strand conformation polymorphisms (SSCP) or denaturing gradient gel electrophoresis (DGGE), can give more accurate answers to fundamental questions on ecosystem diversity. This technique does not however distinguish between active and resting stages, and in order to interpret results accurately, some a priori knowledge of the ecology and function of the organisms is required.

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