Are there any limitations associated with using 16S rDNA as

Solution

Yes, there are limitations associated with using 16S rDNA as a universal genetic marker for prokaryotic organisms as in prokaryotes 16s rRNA gene is conserved between closely related taxonomic groups and cannot be used as a certain marker to resolve among some closely related taxonomic groups. In certain thermophilic archaea 16s rRNA gene contains conserved region that impacts in annealing of universal primers.