Chapter 10 – Classification of Microorganisms

Taxonomy and Taxon

Taxonomy is the science of classifying living organisms, providing a systematic framework for naming, describing, and grouping them based on similarities and differences. A taxon is a category or group used in classification, such as species, genus, or family.

• Taxonomy: The study of classification, including principles, rules, and procedures.

• Taxon: Any rank or group in the classification hierarchy (e.g., genus, species).

• Example: Homo sapiens is a taxon at the species level.

Major Characteristics of the Five Kingdoms

The five-kingdom system classifies organisms based on cell type, complexity, nutrition, and other features.

• Kingdom Procaryotae (Monera): All prokaryotes; lack a nucleus.

• Kingdom Protista: Unicellular eukaryotes; includes protozoa and algae.

• Kingdom Fungi: Includes yeasts, molds, mushrooms; heterotrophic.

• Kingdom Plantae: Multicellular, autotrophic (photosynthetic); includes mosses, ferns, flowering plants.

• Kingdom Animalia: Multicellular, heterotrophic; includes sponges, worms, insects, vertebrates.

Characteristics of Archaea and Eubacteria Domains

Prokaryotes are divided into two domains: Archaea and Eubacteria (Bacteria), distinguished by molecular and structural differences.

• Archaea: Cell walls lack peptidoglycan; unique ribosomal RNA sequences; live in extreme environments; unusual metabolic processes.

• Types of Archaea: Methanogens (produce methane), extreme halophiles (salt-loving), thermoacidophiles (heat and acid-loving).

• Eubacteria: Cell walls contain peptidoglycan; diverse metabolic capabilities; found in many environments.

Scientific Names and Binomial Nomenclature

Organisms are named using binomial nomenclature, which assigns a two-part scientific name: genus and species.

• Genus: Capitalized, noun, italicized or underlined.

• Species: Lowercase, adjective, italicized or underlined.

• Example: Escherichia coli

• Bergey’s Manual: Reference for bacterial classification.

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

Major Taxa and Hierarchical Classification

Taxonomic hierarchy organizes organisms into increasingly broad categories.

• Species: Group of organisms with similar characteristics; in multicellular eukaryotes, can interbreed.

• Genus: Group of related species.

• Family: Group of related genera.

• Order: Group of related families.

• Class: Group of related orders.

• Phylum/Division: Group of related classes.

• Kingdom: Group of related phyla.

• Domain: Highest rank, above kingdom.

In bacteria:

• Four divisions (phyla): One Archaea (unusual cell walls), three Eubacteria (thin gram-negatives, thick gram-positives, wall-less mycoplasmas).

• Strain: Subgroup within a species, derived from a single cell.

Classification of Viruses

Viruses are not included in the five-kingdom system because they are acellular 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 for comparison.

• Identification: Determines the identity of an organism, often for treatment, using minimal procedures.

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

• Morphological characteristics: Limited usefulness; endospores and flagella may help.

Staining and Biochemical Tests for Identification

Staining and biochemical tests are essential for identifying bacteria.

• Differential staining: Distinguishes bacteria based on cell wall composition (e.g., gram stain, acid-fast stain).

• Biochemical tests: Assess enzymatic activities (e.g., carbohydrate fermentation).

• Selective and differential media: Used to speed up identification.

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

• Limitation: Mutations and plasmid acquisition can alter characteristics.

Serological Tests

Serology studies blood serum and immune responses, useful for identifying microorganisms.

• Antigenic: Microorganisms stimulate antibody production.

• Antiserum: Solution of antibodies specific to a microorganism.

• Slide agglutination test: Mixing unknown with antisera; clumping indicates positive result.

• Western blotting: Identifies microbial antigens in patient serum using electrophoresis and antibody tagging.

• Phage typing: Determines susceptibility of bacteria to specific bacteriophages; useful for tracing food-associated infections.

Molecular Methods for Classification

Molecular techniques provide precise tools for classifying and identifying microbes.

• Amino acid sequencing: Compares protein sequences to infer DNA similarity.

• DNA base composition: Percentage of guanine + cytosine () content; fixed for a species.

• DNA fingerprinting: Uses restriction enzymes to cut DNA; fragments separated by electrophoresis.

• Fatty acid profiles: Analyzes cellular fatty acids for classification.

• Ribosomal RNA sequencing: Compares rRNA sequences for evolutionary relationships.

• Polymerase chain reaction (PCR): Amplifies DNA for analysis when organisms cannot be cultured.

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

Dichotomous Keys and Multiple Tests

Dichotomous keys use a series of questions to identify organisms, combining multiple identification methods.

• Each step presents two choices; successive steps narrow down the identity.

• Methods may include morphological, biochemical, serological, and molecular tests.

Summary Table: Major Characteristics of the Five Kingdoms

Summary Table: Differences Between Archaea and Eubacteria

Additional info:

• Modern taxonomy increasingly uses molecular methods (e.g., 16S rRNA sequencing) for classification.

• Viruses are classified separately based on genetic material, structure, and replication strategy.

• Identification is critical in clinical microbiology for diagnosis and treatment.