Classification of Microorganisms: Taxonomy, Phylogeny, and Identification Methods

Chapter 10: Classification of Microorganisms

The Study of Phylogenetic Relationships

Understanding how microorganisms are classified and related is fundamental in microbiology. Two key concepts are taxonomy and phylogeny:

• Taxonomy: The science of classifying organisms, showing the degree of similarity among them.

• Systematics (or phylogeny): The study of the evolutionary history of organisms.

The Three Domains of Life

The three-domain system, developed by Carl Woese in 1978, is based on rRNA sequences and divides all life into:

• Eukarya: Includes animals, plants, fungi, and protists.

• Bacteria: True bacteria, prokaryotic cells.

• Archaea: Includes methanogens, extreme halophiles, and hyperthermophiles.

Key Concepts

• All organisms evolved from cells that formed over 3 billion years ago.

• DNA passed from ancestors is described as conserved.

• Eukarya includes kingdoms Fungi, Plantae, Animalia, and Protists; Bacteria and Archaea are prokaryotes.

Evolution of Eukaryotes: Endosymbiotic Theory

The endosymbiotic theory explains the origin of eukaryotic cells from prokaryotic ancestors:

• Life arose as simple organisms 3.5 to 4 billion years ago.

• First eukaryotes evolved 2.5 billion years ago.

• Larger bacterial cells engulfed smaller ones, leading to mitochondria and chloroplasts.

• Infoldings of the plasma membrane may have formed a true nucleus.

Comparative Characteristics of Domains

Major differences among Archaea, Bacteria, and Eukarya are summarized below:

Feature	Archaea	Bacteria	Eukarya
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Cell Wall	Varies; no peptidoglycan	Contains peptidoglycan	Varies; cellulose/chitin or none
Membrane Lipids	Branched carbon chains	Straight carbon chains	Straight carbon chains
First Amino Acid in Protein Synthesis	Formylmethionine	Formylmethionine	Methionine
Antibiotic Sensitivity	No	Yes	No
rRNA	Lacking	Present	Present

Prokaryotic vs. Eukaryotic Cells and Organelles

Feature	Prokaryotic Cell	Eukaryotic Cell	Eukaryotic Organelles
DNA	One circular chromosome	Linear	Circular
Histones	No	Yes	Yes
First Amino Acid in Protein Synthesis	Formylmethionine	Methionine	Formylmethionine
Ribosomes	70S	80S	70S
Growth	Binary fission	Binary fission	Binary fission

Phylogenetic Trees

Phylogenetic trees group organisms according to common properties, such as:

• Fossils

• Genomes: Mutations accumulated in genomes serve as a molecular clock.

Groups of organisms evolved from a common ancestor, and each species retains some ancestral characteristics.

The Taxonomic Hierarchy

Developed by Linnaeus, the taxonomic hierarchy is a series of subdivisions for classifying organisms:

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

Eukaryotic species: A group of closely related organisms that breed among themselves.

Classification of Prokaryotes

• Prokaryotic species: Population of cells with similar characteristics.

• Culture: Bacteria grown in laboratory media.

• Clone: Population of cells derived from a single parent cell.

• Strain: Genetically different cells within a clone.

Classification of Eukaryotes

• Protista: Catchall kingdom; autotrophic and heterotrophic; grouped into clades based on rRNA.

• Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments.

• Plantae: Multicellular; cellulose cell walls; undergo photosynthesis.

• Animalia: Multicellular; no cell walls; chemoheterotrophic.

Classification of Viruses

• Viruses are not part of any domain and are not composed of cells; they require a host cell.

• Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche.

Methods of Classifying and Identifying Microorganisms

• Classification: Placing organisms in groups of related species using lists of known characteristics.

• Identification: Matching characteristics of an unknown organism to lists of known organisms (e.g., clinical lab identification).

Reference Materials

• Bergey's Manual of Determinative Bacteriology: Provides identification schemes for bacteria and archaea.

• Approved Lists of Bacterial Names: Lists species of known classification.

Clinical Microbiology Lab Practices

• Lab requisition forms are used to note specimen types and tests to be conducted.

• Transport media is used to collect and transport pathogens to a laboratory.

Identification Techniques

• Morphological characteristics: Useful for identifying eukaryotes; limited for phylogenetic relationships.

• Differential staining: Includes Gram staining and acid-fast staining; not useful for bacteria without cell walls.

• Biochemical tests: Determine the presence of bacterial enzymes.

Integrating Classification Methods

• Dichotomous keys: Identification keys based on successive questions.

• Cladograms: Maps showing evolutionary relationships among organisms, based on rRNA sequences.

Biochemical Tests

• Rapid identification methods: Perform several biochemical tests simultaneously; results are assigned numbers.

• Automated rapid identification systems: Available for medically important bacteria and yeast; data from mass spectrophotometry are compared to a database.

Example Table: Biochemical Test Results (Inferred)

Species	Motility	Carbohydrate Use	NO3 Reduction	Opt. Temp. (°C)
Thiobacillus neapolitanus	+	6-8	+	25-30
Thiobacillus ferrooxidans	-	6-7	-	20-30
Paracoccus denitrificans	+	7-9	+	25-30
Additional info: Table entries inferred from context and typical biochemical test results.