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Special Interest Group Meeting

The detection of fungi in soil by molecular based methods

JW Woodhall, IP Adams, JC Peters & N Boonham, The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK

Soils are a habitat for an enormous range of fungi. The use of molecular methods to study fungi in soil offers several advantages over other methods, such as specificity and sensitivity. The application of molecular methods are therefore not only of use in ecological studies but can also have commercial applications. For example, the detection of soil-borne crop pathogens could inform grower decisions concerning planting and soil treatment. However, the successful use of molecular methods to soil is dependent upon a robust soil DNA extraction procedure. A number of PCR inhibitory compounds exist in the soil and consequently a diverse range of extraction procedures and are employed to overcome this issue. Sampling strategies also influence the successful detection of particular fungal species. The analysis of soil DNA is typically with real-time PCR, which in conjunction with a robust soil extraction method, can detect as little as  10−7 g fungal material per g of soil.  The optimisation of sampling strategies and DNA extraction procedures are discussed. In addition to the use of real-time PCR, next generation sequencing (pyrosequencing) has been undertaken on soil DNA to determine the breadth of fungal species present and this methodology is also discussed.