Classification of Microorganisms & Prokaryotic Diversity: Study Notes

Ch. 10: Classification of Microorganisms

Taxonomy: Organizing Life

Taxonomy is the science of classifying organisms into hierarchical categories called taxa. This process helps scientists understand evolutionary relationships and organize biological diversity.

• Systematics/Phylogeny: The study of evolutionary relationships among organisms.

• Taxonomic Hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. Mnemonic: "Dear King Philip Come Over For Good Spaghetti".

• Subspecies, Strains, Serovars: Additional subdivisions used for finer classification, especially in microbiology.

Three Domains of Life

All organisms are classified into three domains: Bacteria, Archaea, and Eukarya. Each domain is characterized by unique cellular and molecular features.

• Bacteria: Prokaryotic, cell walls contain peptidoglycan.

• Archaea: Prokaryotic, cell walls lack peptidoglycan, often extremophiles.

• Eukarya: Eukaryotic, includes animals, plants, fungi, and protists.

Methods of Classification

Microorganisms are classified using a variety of methods, each providing different information about their identity and relationships.

• Conventional Classification: Based on morphology (shape, size, color, interactions, external & internal features).

• Differential Staining: Includes Gram stain, acid-fast stain (for Mycobacterium tuberculosis), and endospore stain.

• Biochemical Tests: Assess metabolic capabilities, enzyme presence, and waste products.

• Serology: Uses antigen-antibody interactions to identify microbes.

• Fatty Acid Profiles (FAME): Unique fatty acid composition of bacteria.

• DNA & RNA Sequencing: Determines genetic relationships and identifies unique sequences.

Conventional Classification: Morphology & Staining

Microbial morphology and staining techniques are fundamental for initial identification.

• Shape: Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral-shaped).

• Gram Stain: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink).

• Acid-fast Stain: Used for bacteria with waxy cell walls, such as Mycobacterium tuberculosis.

• Endospore Stain: Identifies spore-forming bacteria.

Biochemical Tests

Biochemical tests are performed on bacterial cultures to determine their metabolic properties.

• Oxygen Use: Aerobic vs. anaerobic metabolism.

• Metabolic Fuel Use: Utilization of sugars, amino acids, etc.

• Enzyme Presence: Detection of specific enzymes (e.g., catalase, oxidase).

• Waste Products: Identification of metabolic byproducts.

Rapid Identification Systems

Systems like EnteroPluri allow rapid identification of enteric bacteria by testing multiple biochemical reactions simultaneously.

Serology

Serological methods use antigen-antibody interactions to identify microorganisms and their strains.

• Antiserum: Contains antibodies against specific antigens.

• Serovar/Serotype: Variants within a species distinguished by antigenic properties.

• COVID Test: Detects antibodies or antigens using lateral flow immunoassay.

Phage Typing

Phage typing uses bacteriophages to identify bacterial strains based on susceptibility to specific viruses. Useful for tracing outbreaks.

• Applications: Mycobacterium tuberculosis, Yersinia pestis, Bacillus anthracis, Staphylococcus aureus.

Fatty Acid Profiles (FAME)

Each bacterial species has a unique profile of fatty acids, which can be analyzed by gas chromatography after conversion to methyl esters.

• FAME Analysis: Fatty Acid Methyl Ester analysis is used for bacterial identification.

DNA & RNA Sequencing

Genetic methods provide precise identification and classification of microorganisms.

• Whole Genome Sequencing: Comprehensive but resource-intensive.

• DNA-DNA Hybridization: Measures genetic similarity between organisms.

• DNA Microarray: Detects specific DNA sequences or genes.

• DNA Fingerprinting: Identifies unique genetic patterns.

• Fluorescent In Situ Hybridization (FISH): Stains specific DNA or RNA sequences in cells.

Ch. 11: The Prokaryotes: Domains Bacteria and Archaea

Domain Archaea

Archaea are prokaryotes distinct from bacteria, often found in extreme environments. They lack peptidoglycan in their cell walls and have unique membrane lipids and DNA sequences.

• Extremophiles: Thrive in extreme conditions (e.g., high temperature, salinity).

• No Known Human Pathogens: Archaea are not associated with human disease.

Domain Bacteria

Bacteria are prokaryotes with diverse metabolic and ecological roles. They are classified based on cell wall structure, metabolism, and genetic characteristics.

• Gram Negative Bacteria: Phylum Pseudomonadota (Proteobacteria) is the largest group, mostly chemoheterotrophs.

• Classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria.

Alphaproteobacteria

• Rhizobium: Nitrogen-fixing bacteria important for legumes (beans, peas, clover).

• Rickettsia: Transmitted by insects and ticks; causes Rocky Mountain Spotted Fever and Typhus.

• Wolbachia: Inhibits insect reproduction; used for mosquito control to prevent Zika & Dengue.

Betaproteobacteria

• Bordetella: Causes pertussis (whooping cough).

• Neisseria: Cocci inhabiting mucous membranes; causes gonorrhea.

Summary Table: Characteristics of Archaea, Bacteria, and Eukarya

Feature	Archaea	Bacteria	Eukarya
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Cell Wall	Varies, no peptidoglycan	Contains peptidoglycan	Varies, no peptidoglycan
Membrane Lipids	Branched carbon chains	Straight carbon chains	Straight carbon chains
First Amino Acid in Protein Synthesis	Methionine	Formylmethionine	Methionine
Antibiotic Sensitivity	No	Yes	No
RNA Polymerase	Several types	One type	Several types
Common tRNA for Met	Lacking	Present	Present

Taxonomic Hierarchy Example

Domain	Kingdom	Phylum	Class	Order	Family	Genus	Species
Eukarya	Fungi	Ascomycota	Hemiascomycetes	Saccharomycetales	Saccharomycetaceae	Saccharomyces	S. cerevisiae
Archaea	None assigned	Euryarchaeota	Methanococci	Methanococcales	Methanococcaceae	Methanococcus	M. okinawensis
Bacteria	None assigned	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	E. coli