You can use DI water and pickup the bacterial colony mix in the water use as template for RT-PCR,

Thanks,

So you think it would be good enough for such a sensitive technique as qPCR? That is what I am planning on doing but I am afraid of any interference that can possibly inhibit the reaction. I know that regular PCR work just fine with this technique but I was not sure about qPCR

Did you consider a simple phenol, phenol chloroform, phenol chloroform isoamyl alcohol extraction, followed by ethanol precipitation?  It is an organic extraction which generates organic waste but it would certainly work well.

Hi Thanh!

I usually use a kit (AxyPrep) to extract DNA from plant bacteras for qPCR applications, but some times I use CTAB protocol without phenol and it works too. I compared the sensibility of the essay using DNA extracted by both methods but with the same sample and I found small differences in the Ct values. 

Dear Thanh

The response depends a lot of the end use of this PCR. If you're doing a PCR from a single colony, DI water and boil, or microwate will be good. If you're working with real samples, and gram negative bacteria, at least use a chellex based procedure. 

best regards