Use of 16S rRNA sequences

It’s a universal marker which comprises both variable and conserved regions; - variable regions can be used to derive relatedness, and serve as phylogenetic chronometers. It can be selectively amplified depending on the taxonomic resolution needed. It constitutes more than 95% of the total cellular RNA content and possesses a rather large size (1.5 kb). This molecule is also ecologically relevant since the cell content of rRNA, which can be quantified using in situ hybridization, provides an index of the metabolic activity and growth rate of a population