Classification of Microorganisms

Introduction to Taxonomy and Phylogeny

Taxonomy is the science of classifying organisms to reflect their similarities and evolutionary relationships. Systematics, or phylogeny, studies the evolutionary history of organisms, grouping them based on common ancestry and genetic relationships. Accurate classification is essential for communication, research, and understanding microbial diversity.

The Development of Classification Systems

Historical Perspectives

• Linnaeus (1735): Introduced the two-kingdom system (Plantae and Animalia).

• Von Nägeli & Haeckel (1800s): Proposed bacteria and fungi as plants; Haeckel added Protista for microorganisms.

• Whittaker (1969): Developed the five-kingdom system, including Monera (prokaryotes), Protista, Fungi, Plantae, and Animalia.

• Woese (1978): Proposed the three-domain system based on rRNA sequencing: Bacteria, Archaea, and Eukarya.

Limitations of Early Systems

• Two-kingdom and five-kingdom systems did not account for fundamental differences between prokaryotes and eukaryotes.

• Molecular evidence (e.g., rRNA sequences) revealed deeper evolutionary divisions, leading to the three-domain system.

The Three-Domain System

Overview of Domains

The three-domain system classifies all life into Bacteria, Archaea, and Eukarya, reflecting major differences in cell structure, genetics, and biochemistry.

• Bacteria: True bacteria, prokaryotic, peptidoglycan cell walls.

• Archaea: Prokaryotic, no peptidoglycan, often extremophiles (e.g., methanogens, halophiles, hyperthermophiles).

• Eukarya: Eukaryotic organisms, including animals, plants, fungi, and protists.

Key Characteristics of Domains

Endosymbiont Theory

The endosymbiont theory explains the origin of eukaryotic organelles. Eukaryotes evolved when ancestral prokaryotic cells engulfed other prokaryotes, which became mitochondria and chloroplasts. This is supported by similarities in DNA, ribosomes, and division methods between these organelles and bacteria.

Phylogenetic Relationships and Evidence

Phylogenetic Trees

Phylogenetic trees group organisms based on evolutionary relationships, using evidence such as fossils and molecular data (e.g., rRNA and genome sequencing). Mutations accumulate at a constant rate, providing a molecular clock for evolutionary studies.

Taxonomic Hierarchy and Nomenclature

Scientific Nomenclature

Binomial nomenclature assigns each organism a two-part name: genus and specific epithet (species). This system, used worldwide, avoids confusion caused by common names and language differences. For example, Salmonella enterica honors Daniel Salmon and indicates its presence in the intestines.

Taxonomic Hierarchy

The taxonomic hierarchy is a series of subdivisions used to classify organisms:

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

Classification of Prokaryotes and Eukaryotes

Prokaryotes

Bergey’s Manual of Systematics of Archaea and Bacteria is the standard reference for prokaryotic classification. Prokaryotic species are populations of cells with high genomic similarity. Key terms:

• Culture: Bacteria grown in laboratory media.

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

• Strain: Genetically different cells within a clone.

Eukaryotes

• Protista: Mostly unicellular, nutritionally diverse, grouped by rRNA clades.

• Fungi: Chemoheterotrophic, chitin cell walls, develop from spores or hyphae.

• Plantae: Multicellular, cellulose cell walls, photosynthetic.

• Animalia: Multicellular, no cell walls, ingest organic matter.

Viruses

Viruses are not classified within any domain because they are not composed of cells and require a host for replication. Viral species are defined by shared characteristics and can be distinguished by morphology, genome, enzymes, and ecological niche.

Methods of Classifying and Identifying Microorganisms

Classification vs. Identification

• Classification: Placing organisms into groups of related species based on lists of characteristics.

• Identification: Matching characteristics of an unknown organism to known organisms, often in clinical labs.

Bergey’s Manual of Determinative Bacteriology

This manual provides identification schemes for bacteria and archaea, using criteria such as morphology, cell wall composition, differential staining, oxygen requirements, and biochemical testing.

Conventional Identification Methods

• Morphology: Useful for eukaryotes; presence of endospores or flagella can aid identification.

• Differential Staining: Gram and acid-fast stains; not useful for bacteria without cell walls or archaea.

• Biochemical Tests: Detect enzymatic activities; rapid identification systems can test multiple enzymes simultaneously.

Serological Methods

• Serology: Study of serum and immune responses; microorganisms are antigenic and stimulate antibody production.

• Slide Agglutination Test: Bacteria clump when mixed with specific antibodies, differentiating species and strains.

• ELISA (Enzyme-Linked Immunosorbent Assay): Detects antigens or antibodies; used for rapid diagnostics (e.g., COVID-19, HIV).

Phage Typing

Phage typing determines which bacteriophages a bacterium is susceptible to. Plaques (clearings) on a plate indicate lysis by specific phages, useful for tracing infection sources.

Molecular and Genomic Methods

• Fatty Acid Methyl Ester (FAME) Analysis: Fatty acid profiles are species-specific.

• Protein Profiling (MALDI): Mass spectrometry compares protein profiles to databases.

• Flow Cytometry: Differentiates cells by fluorescence or electrical properties without culturing.

• Whole Genome Sequencing: Compares DNA base composition (G+C content) for relatedness.

Nucleic Acid Hybridization Techniques

• DNA-DNA Hybridization: Measures the degree of hybridization between DNA strands; >70% indicates same species.

• PCR (Polymerase Chain Reaction): Amplifies DNA for identification, even from unculturable organisms.

• Southern Blotting: Uses DNA probes to identify specific sequences in unknown samples.

• DNA Chips (Microarrays): Detect pathogens by hybridization and fluorescence.

• Ribotyping: Uses rRNA sequencing for classification.

• FISH (Fluorescent In Situ Hybridization): Uses fluorescent probes to stain and identify microorganisms in situ.

Identification Tools

• Dichotomous Keys: Stepwise identification using paired questions.

• Cladograms: Diagrams showing evolutionary relationships based on genetic similarity.

Summary Table: Key Differences Among Domains

Additional info: This summary integrates foundational concepts in microbial taxonomy, phylogeny, and identification, providing a comprehensive overview for microbiology students preparing for exams or coursework.