How to deal with the interference between bacterial 16SrDNA and plastid ribosoma - (Jun/06/2014 )

I need to quantify Actinobacteria and total Eubacterial community in potato skin. for Actinobacteria it was done by a pair of specific primer that covers actinobacterial 16SrDNA. but for quantification of Eubacteria the interference between bacterial 16SrDNA and plastid ribosomal DNA is a problem. is there any idea? 

How similar are the plastid and eubacterial sequences?  It may be that you could re-design the primers.

Hi,

yes thanks, you were right.  several internal primers that could cover only the eubacterial gene were  designed based on a small difference in the middle of the gene.