Quantification of Pythium populations in ginseng soils - Mount Saint ...

applied soil ecology 40 (2008) 447–455 453Fig. 3 – Percentages of P. irregulare colonies possessing PiF/PiR qPCR primer sites (black) in each of the seven naturallyinfested soils. Data based on ITS sequences of dilutionplate colonies obtained using universal primers. Thenumber of colonies sequenced per soil is given at the topof each bar.Fig. 5 – Target DNA concentrations (black) compared to CFUdata (grey) in each of the seven naturally infested soils. (a)P. irregulare DNA VS CFU/100 mg dry soil; CFU dataadjusted to reflect the proportion of isolates possessingqPCR primer sites. (b) P. ultimum DNA VS CFU/100 mg drysoil. Each bar represents an average of threemeasurements. Error bars represent the standard error ofthe mean.naturally occurring P. irregulare populations are somewhathigher than those of P. ultimum, while the average concentrationof P. irregulare DNA was much lower than that of P. ultimumDNA (Fig. 5).4. DiscussionFig. 4 – Target DNA concentrations compared to numbers ofcolony forming units in dilution series of artificiallyinfested soils. (a) Pythium irregulare DNA VS P. irregulareCFU/100 mg dry soil. (b) Pythium ultimum DNA VS P.ultimum CFU/100 mg dry soil. Error bars represent thestandard error of the mean.We have used both real-time PCR and dilution plating onselective media in order to estimate populations of P. irregulareand P. ultimum in ginseng soils in south-western Ontario. Ingeneral, there was good agreement between the data setsproduced using the two techniques. However, the directcomparison of qPCR and dilution plate data proved difficult forP. irregulare, due to the presence of cryptic species within the‘‘P. irregulare complex’’ (Garzón et al., 2007).Our qPCR primers for P. irregulare were designed to targetthe most common members of the P. irregulare complex;essentially those defined by Matsumoto et al. (2000) as ‘‘GroupI’’ and ‘‘Group II’’ and more recently by Garzón et al. (2005) as P.irregulare sensu stricto. However, sequences from P. irregulare