Classification of Microorganisms: Taxonomy, Domains, and Identification Methods

Chapter 10 – Classification of Microorganisms

Taxonomy and Taxa

Taxonomy is the scientific discipline concerned with classifying and naming living organisms. It provides a universal language for biologists and a framework for understanding the relationships among organisms.

• Taxonomy: The science of classification of living forms.

• Taxon (plural: taxa): A category used to classify organisms according to degrees of similarity (e.g., species, genus, family).

• Purpose: Organizes biological diversity and reflects evolutionary relationships.

Major Characteristics of the Five Kingdoms

Organisms are traditionally classified into five kingdoms based on cellular organization, nutritional patterns, and other characteristics.

• Kingdom Procaryotae (Monera): All prokaryotes (bacteria and archaea).

• Kingdom Protista: Unicellular eukaryotes (e.g., protozoa, some algae).

• Kingdom Fungi: Includes unicellular yeasts, multicellular molds, and mushrooms; all are heterotrophic.

• Kingdom Plantae: Includes some algae, all mosses, ferns, conifers, and flowering plants; all are multicellular and autotrophic (photosynthetic).

• Kingdom Animalia: Includes sponges, worms, insects, and vertebrates; all are multicellular and heterotrophic.

Domains: Archaea and Eubacteria

Prokaryotes are divided into two domains based on genetic and biochemical differences.

• Archaea: Differ from Eubacteria in ribosomal RNA sequences, lack peptidoglycan in cell walls, often inhabit extreme environments, and have unique metabolic pathways.

• Types of Archaea:

  • Methanogens: Produce methane from CO2 and H2.

  • Extreme halophiles: Thrive in high-salt environments.

  • Thermoacidophiles: Live in hot, acidic environments.

• Eubacteria: True bacteria, with peptidoglycan in cell walls.

Scientific Names (Binomial Nomenclature)

Organisms are named using a two-part system called binomial nomenclature.

• Genus: Always capitalized and a noun.

• Species: Lowercase and usually an adjective.

• Both names are italicized or underlined (e.g., Escherichia coli).

• Bergey’s Manual of Systematic Bacteriology: Reference for bacterial classification.

• Order suffix: -ales; Family suffix: -aceae.

Major Taxa and Hierarchical Classification

Organisms are classified in a hierarchical system from broad to specific categories.

• Hierarchy (from broadest to most specific): Domain > Kingdom > Phylum (Division) > Class > Order > Family > Genus > Species

• Bacterial Divisions/Phyla:

  • One division: Archaea (unusual cell walls)

  • Three divisions: Eubacteria (thin gram-negatives, thick gram-positives, wall-less bacteria such as mycoplasmas)

• Species (Eukaryotes): Group of organisms that can interbreed.

• Species (Bacteria): Population of cells with similar characteristics; strains are subgroups derived from a single cell.

Classification of Viruses

Viruses are not classified within the five-kingdom system because they are not cellular and require host cells for replication.

• Viral species: Population of viruses with similar characteristics (morphology, genes, enzymes).

Classification vs. Identification

Classification and identification are related but distinct processes in microbiology.

• Classification: Organizes organisms based on shared characteristics and evolutionary relationships.

• Identification: Determines the identity of an organism, often for clinical or practical purposes, using minimal tests.

• Bergey’s Manual of Determinative Bacteriology: Used for identification based on cell wall composition, morphology, staining, oxygen requirements, and biochemical tests.

• Morphological characteristics: Limited usefulness due to similarities among species; endospore and flagella morphology can sometimes help.

Staining and Biochemical Tests for Bacterial Identification

Laboratory techniques are essential for identifying bacteria.

• Differential staining: First step in identification; includes Gram stain and acid-fast stain.

• Stains are based on cell wall composition; not useful for mycoplasmas or archaea.

• Biochemical tests: Differentiate bacteria based on enzymatic activities (e.g., carbohydrate fermentation).

• Selective and differential media: Aid in identification.

• Rapid identification tools: Perform multiple tests simultaneously; results in 4–24 hours.

• Limitations: Mutations and plasmid acquisition can alter characteristics; rapid tools also exist for yeasts and fungi.

Serological Tests

Serology involves the study of immune responses in blood serum and is used for microbial identification.

• Antigenic properties: Microorganisms stimulate antibody production.

• Antiserum: Solution of antibodies specific to a microorganism.

• Slide agglutination test: Unknown organism mixed with antisera; clumping indicates a positive reaction.

• Western blotting: Identifies microbial antigens in patient serum using electrophoresis and antibody-dye conjugates.

• Phage typing: Determines susceptibility of bacteria to specific bacteriophages; useful in epidemiology.

Molecular Methods for Microbial Classification

Molecular techniques provide precise tools for classifying and identifying microorganisms.

• Amino acid sequencing: Compares protein sequences to infer genetic relatedness.

• DNA base composition: Expressed as %G+C content; reflects genetic similarity.

• DNA fingerprinting: DNA is cut with restriction enzymes, fragments separated by electrophoresis, and patterns compared.

• Other molecular markers: Fatty acid profiles, ribosomal RNA sequencing.

• Polymerase Chain Reaction (PCR): Amplifies microbial DNA for analysis, especially when organisms cannot be cultured.

• Nucleic acid hybridization: Measures similarity between DNA from different organisms by hybridizing single strands; fluorescent probes can detect specific pathogens (e.g., Salmonella in food).

• Dichotomous keys: Stepwise identification using paired questions and multiple methods.

Summary Table: Major Taxonomic Ranks and Examples

Rank	Suffix (if applicable)	Example
Domain	-	Bacteria, Archaea, Eukarya
Kingdom	-	Animalia, Plantae, Fungi, Protista, Monera
Phylum/Division	-phyta (plants), -mycota (fungi)	Proteobacteria (bacteria), Ascomycota (fungi)
Class	-ae	Gammaproteobacteria
Order	-ales	Enterobacteriales
Family	-aceae	Enterobacteriaceae
Genus	-	Escherichia
Species	-	Escherichia coli

Key Equations and Concepts

• DNA Base Composition (%G+C):

$\text{Percent G+C} = \frac{\text{Number of G and C bases}}{\text{Total number of bases}} \times 100$

• Polymerase Chain Reaction (PCR): Amplifies DNA exponentially using cycles of denaturation, annealing, and extension.

Example Applications

• Clinical identification: Rapid identification tools and serological tests are used to diagnose infections quickly.

• Food safety: DNA probes detect pathogens like Salmonella in food samples.

• Epidemiology: Phage typing and DNA fingerprinting track sources of outbreaks.

Additional info: Modern taxonomy increasingly relies on molecular data (e.g., 16S rRNA sequencing) to resolve evolutionary relationships, especially among prokaryotes.