I am sorry, your question is concerned with colony PCR? because I can not correlare the bacterial growth medium and polymerase chain reaction.
If I understood question correctly: You are asking about culturable and unculturable Environmental Pathogens?
The adv. of PCR/DGGE technique is that it can be used for identification of Microbes by either way - culturable or unculturable. The identification will be complete till the genus species level (which will be needed for a good publication). Limitation is one has to know specific primers!!
Whereas, use of bacterial media - enrichment/ growth/ biochemical tests are also not obsolete yet. It will definetly give you some idea about metabolism of the microbes, which may be needed to understand the mechanism for the control of Pathogen. But limitation of media is only culturable population will be identified, that too till genus level, with good accuracy.
So, one has to go for both techniques: Biochemical/ media based technique and Molecular tools ..
I hope I understood your question correctly!
Thank you both Sanket and Ananda. What is wish to know is if there is 1000 E. coli cells in 1 liter of water and harvest 10 milliliter and plate this on TSA, I should get 10 colonies. Is it possible to do PCR and get a concordance with the plate assay?
As far as I know, MPN OR Plate assys can give you idea about the cfu/ml, but PCR can only give you idea about presence of particular microorganism, not the numbers. PCR will only confirm that the colony you obtained is of E. coli or whatever organism you intend to identify.
Yes, you can do a PCR to determine the numbers of bacteria in a suspension, but you will need to do a quantitative PCR (qPCR), a special form of PCR. There are several ways to do qPCR. A very often used version uses two primers, such as in regular PCR, as well as a probe (a third, labeled, oligo that will fit somewhere in between the 2 primers). The qPCR is performed in a "real time" PCR machine, that measures the incorporation of the probe into the PCR product. In order to determine how much PCR product is made, you will also do a standard curve on known quantities of the PCR target, so you can correlate the amount of probe signal to the amount of bacteria in the solution. There are many different variants to this qPCR, so I have just described it in general terms. You can do either a specific PCR (e.g. to detect E. coli only) or a broad-range bacterial PCR (on the 16S rRNA gene, to detect all bacteria), or combine these two to get a ratio. I hope this helps!
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