This is actually a tricky question. In general, both culture-based and PCR based techniques have their pro and cons, and maybe you should use both and compare the results. PCR should give you a pretty accurate quantification of the gene your primers are amplifying. However, results depend on copy number of the gene per genome, and nuclei per organism (and you need a reliable standard curve for interpretation of your ct values). PCR will also amplify genes of dead or inactive microbes. On the other hand, culture techniques will give you only a rough estimation of the cfu and might lead to overestimation of heavily sporulating isolates over non-sporulating isolates. However, as in many quantitative approaches, sampling might be the most crucial step for obtaining reliable results. ELISA should not be used for quantification.

Thanks, I have done nested PCR to confirm the identity of Phytophthora species. I want to quantify through real time PCR, for amount of fungus on roots. But for cultural techniques, I have tried plating roots on PARPH, is there another reliable cultural technique to quantify the propagule or assess root damage due to the Phytophthora.

Working with mRNA You emphasize on the use of living Phytophthora biomass. You use cDNA as the template for Real Time PCR. PARPH is also a reliable medium for working with Phytophthora spp. However, I think if You are working with seedlings, the amount of propagule will not be much important under conducive conditions of the experiment as the oomycetous pathogen is enough fast growing to compensate the differences in propagule rates in time, and colonize the root system of the plants. Such differences are expected to be important in citrus groves with well-established older trees where propagule rate affects the pathogen distribution in soil. But if You are interested in studying of the propagule density impact on root infection progress, You may first prepare a chlamydospore suspension with a determined number of chlamydospores per 10 microliters. You may prepare different paper discs harboring different numbers of chlamydospores through different levels of concentrations, 1 time 10 ul/disc, 10x10 ul/ disc, 100x10 ul/ disc. Evaporate or filter the liquid phase instantly and do not allow chlamydospores to germinate. use the discs as the inoculation units of different densities (with enough plants and enough discs for each density required to do real-time studies of disease progress in/on main root (simply a little under crown) and to calculate Areas Under Disease Progress Curves for each case. I hope this simple method is helpful.