Comprative Quant PCR method on RNA question

[koze99]

I understand that 99% of the RNA isolated with my total RNA isolation kit (qbio problu kit) is rRNA. I am going to quantitate mRNA for specific genes and compare to 16S expression. Do my 16S primers amplify only mRNA for 16S or also all the rRNA? Stupid question maybe but I am confused on some recent studies that indicate over 1000x relative expression to the 16S which should be impossible if rRNA is amplified??

for example:

http://aem.asm.org/cgi/content/abstract/73/8/2491

and

http://mic.sgmjournals.org/cgi/content/ ... /153/1/102

thank you