Quantifying potato pathogen DNA in soil

An improved method for the direct extraction of DNA from soil involving processing of a relatively large sample (60 g) was developed. The accurate and reliable detection and quantification of the soil-borne potato pathogens Colletotrichum coccodes (black dot), Rhizoctonia solani (black scurf) and Spongospora subterranea (powdery scab) following inoculation of soils was demonstrated. With this method, low levels of target DNA (30-40 pg DNA/g soil) could be detected in field soils. DNA recovery was proportionate across a wide range of inoculum (R2 > 0.86) and there was no effect of soil type on the recovery of C. coccodes. The method was used to assess levels of naturally occurring pathogen DNA in 122 soil samples obtained from commercial potato fields.