How did ribosomal RNA research change the classification of microorganisms?

Ribosomal RNA (rRNA) research fundamentally transformed the classification of microorganisms by shifting the basis of taxonomy from observable physical traits (morphology) to evolutionary history (phylogeny).1

In the late 1970s, microbiologist Carl Woese utilized 16S rRNA sequence analysis to compare organisms at a molecular level. Because rRNA is present in all cells and evolves very slowly, it serves as a reliable "molecular chronometer" for determining evolutionary relatedness. This research led to several major changes:1234

• The Three-Domain System: rRNA analysis revealed that prokaryotes are not a single, uniform group. It demonstrated that Archaea are as genetically distinct from Bacteria as they are from Eukarya, leading to the replacement of the older five-kingdom system with the three-domain classification.312
• Correction of Misclassifications: Molecular data exposed the limitations of relying on phenotypic traits. For example, organisms like Mycoplasma were found to be related to specific gram-positive bacteria despite lacking a cell wall, a trait that had previously obscured their true evolutionary position.3
• Refining Eukaryotic Taxonomy: rRNA studies have also reshaped the classification of protists, leading many scientists to abandon the kingdom Protista as a valid grouping in favor of more accurate phylogenetic supergroups.12