Have you tried to change the primers. also try to make sure you have extract the right DNA samples, find some new protocols and try to compare between them.

Hi: What are the concentration and quality of DNA after the extraction from bacteria?

How much is your primer stock concentration? I think the problem is in your PCR master mix. And how you extract your DNA?

Dear Scientists,

Thank you for your kind comments. I extracted the DNA directly from 48 hours grown bacterial culture (Nutrient broth) using isolation Kit and also extracted DNA from infected plant's leaf tissue using CTAB protocol. The extracted DNA of Xanthomonas axonopodis pv.citri grown in nutrient broth was quantified using Nanodrop-2000. 

Concentration = 39.8 ng/ul

Quality = 1.70 

I am waiting for your kind help. Thank you.  

Its look your DNA extraction is good, check with your PCR master mix, some time if it is not good quality it will give bad results. 

Hi Muhammad!  I used to have problems with that to. Try to use DMSO (6%) in your PCR master mix, it might help a little.  About the temperaturate, I used a gradient  PCR from 65ºC to 72ºC. Ask me if you need any help. 

Talk to a colleague about your PCR recipe. It doesn't look correct. I think your primers are too concentrated and the amounts of buffer, MgCl, etc don't sound correct. Honestly, just buy a ready to use PCR mix where the buffer, enzyme and dNTPs are all included. They are really cheap now.

Also, try trouble-shooting one set of primers at a time. Include a good positive DNA control and a water negative control every time. Chances are that each set of primers will have a different annealing temperature. Good luck!