Classification of Microorganisms: Taxonomy, Phylogeny, and the Three-Domain System

Classification of Microorganisms

Taxonomy

Taxonomy is the science of classifying organisms. It organizes living things into categories called taxa based on similarities and differences, providing a universal system for naming and identifying organisms.

• Taxa: Hierarchical groups used to classify organisms (e.g., species, genus, family).

• Universal Names: Scientific names avoid confusion caused by common names and provide a standard reference.

• Identification: Taxonomy helps in identifying organisms by referencing their classification.

Example: Escherichia coli is universally recognized, whereas 'coliform bacteria' may refer to several species.

Systematics, or Phylogeny

Systematics (phylogeny) is the study of the evolutionary history and relationships among organisms. It seeks to understand how species are related through common ancestry.

• Evolutionary History: Traces the lineage of organisms over time.

• Conserved DNA: Genetic material passed down from ancestors is described as conserved.

• Species Diversity: Over 1.5 million species identified; estimates suggest 10–100 million may exist.

Example: The evolutionary tree shows how bacteria, archaea, and eukaryotes diverged from a common ancestor.

Foundations of Classifying Bacteria

Historical Kingdoms and Domains

Early classification systems included only Plantae and Animalia. As knowledge expanded, new kingdoms and domains were proposed to accommodate microorganisms.

• Kingdom Protista: Proposed for bacteria, protozoa, algae, and fungi.

• Prokaryote: Term introduced for cells lacking a nucleus.

• Kingdom Fungi: Recognized for fungi.

• Kingdom Prokaryotae (Monera): Proposed for prokaryotic organisms.

• Two Types of Prokaryotes: Bacteria and Archaea.

• Three-Domain System: Bacteria, Archaea, Eukarya.

Example: The three-domain system reflects fundamental differences in cell structure and genetics.

The Three-Domain System

Overview of Domains

The three-domain system is the most widely accepted classification for all life forms, based on differences in ribosomal RNA, cell structure, and biochemistry.

• Eukarya: Includes all eukaryotes (organisms with a true nucleus), such as protists, fungi, animals, and plants.

• Bacteria: Prokaryotes with peptidoglycan in their cell walls; includes most known bacteria.

• Archaea: Prokaryotes without peptidoglycan; often found in extreme environments (high salt, temperature, or acidity).

Example: Halobacterium (Archaea) thrives in highly saline environments, while Staphylococcus aureus (Bacteria) is common on human skin.

Table: Key Characteristics of the Three Domains

Domain	Cell Type	Cell Wall Composition	Typical Organisms	Environment
Bacteria	Prokaryotic	Peptidoglycan	Bacteria (e.g., E. coli)	Wide range (soil, water, body)
Archaea	Prokaryotic	No peptidoglycan	Archaea (e.g., Halobacterium)	Extreme (salty, hot, acidic)
Eukarya	Eukaryotic	Varied (cellulose, chitin, none)	Protists, fungi, plants, animals	Wide range

Additional info:

• The three-domain system is based primarily on differences in 16S/18S rRNA sequences.

• Domains are the highest taxonomic rank, above kingdoms.