I can not understand your study design exactly. The amount of RNA and DNA of eukaryote is too big compared to prokaryote RNA and DNA. In usual study design like clinical samples, you put the only same amount of nucleotide microgram or same amount of eukaryote nucleotide cells, and only quantization of bacterial mRNA and DNA is enough.

If you want to know bacteria amount in your sample with dead or alive, you should make the universal bacterial primers targeting the DNA. If you want to know the active bacteria and their activity, you should make the universal bacterial primers targeting the mRNA.

I am sorry that I have no idea about the recommended sequence for universal primers.

Hello

Quantifying bacterial load using qPCR on mRNA is not recommended. You need to use a more relevant method. DNA copy number (targeting a single gene) has a higher correlation with bacterial load.

All the best

In this paper you can find 16Suniversal primers for qPCR.

Hope this helps