Microbial Phylogeny and the Three Domains

Comparing conserved molecular sequences reorganized the tree of life into three domains and placed microorganisms at its foundation, revealing archaea as a lineage as distinct from bacteria as from eukaryotes.

Definition

Microbial phylogeny is the reconstruction of evolutionary relationships among microorganisms from molecular data, and the three-domain system is the resulting classification of cellular life into Bacteria, Archaea, and Eukarya.

Scope

This topic covers the use of ribosomal RNA and other conserved molecules as molecular chronometers; the construction and interpretation of phylogenetic trees; the recognition of the three domains, Bacteria, Archaea, and Eukarya; and the implications of this framework for classifying microbial diversity and inferring deep evolutionary relationships.

Core questions

• How can molecular sequences reveal evolutionary relationships?
• Why is ribosomal RNA used as a molecular chronometer?
• What evidence supports three domains rather than two?
• How does phylogeny inform microbial classification?

Key concepts

• Molecular chronometers
• Ribosomal RNA phylogeny
• Phylogenetic trees
• Bacteria, Archaea, and Eukarya
• Universal tree of life

Key theories

Three-domain hypothesis

Ribosomal RNA sequence comparisons by Woese and Fox showed that archaea form a domain distinct from bacteria and eukaryotes, establishing three primary lineages of cellular life.

Mechanisms

Because genes such as those encoding ribosomal RNA are present in all cellular life, change slowly, and are functionally constant, differences in their sequences reflect the time since lineages diverged. Aligning these sequences and analyzing the patterns of difference produces phylogenetic trees, which placed archaea on a branch separate from both bacteria and eukaryotes and yielded the universal three-domain tree.

Clinical relevance

The molecular phylogenetic framework underlies modern microbial classification and identification, allows microbes to be placed in evolutionary context from sequence data alone, and provides the basis for interpreting the diversity revealed by environmental sequencing.

History

In 1977 Carl Woese and George Fox reported that comparisons of ribosomal RNA sequences distinguished a group they called archaebacteria from other bacteria, leading to the three-domain system that replaced the simple prokaryote-eukaryote dichotomy.

Key figures

• Carl Woese
• George Fox

Seminal works

• woese1977
• madigan2018

Frequently asked questions

Why is ribosomal RNA used to study microbial evolution?

Ribosomal RNA genes are present in all cellular organisms, perform the same essential function, and change slowly over time. These properties make their sequences reliable records of evolutionary history that can be compared across very distant lineages.