Chapter 10: Classification of Microorganisms

The Study of Phylogenetic Relationships

Understanding how microorganisms are classified is fundamental in microbiology. This process involves taxonomy and systematics, which help organize and trace the evolutionary history of organisms.

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

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

• Example: Classification of bacteria based on genetic and morphological similarities.

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 three major domains.

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

• Bacteria: True bacteria, prokaryotic organisms.

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

• Key Concept: All organisms evolved from cells that formed over 3 billion years ago. DNA passed from ancestors is described as conserved.

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.

• Endosymbiosis: Larger bacterial cells engulfed smaller ones, which became organelles such as mitochondria and chloroplasts.

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

• Example: Mitochondria and chloroplasts have their own DNA, supporting the endosymbiotic origin.

Comparative Characteristics of Domains

Archaea, Bacteria, and Eukarya differ in several cellular features.

Prokaryotic Cells vs. Eukaryotic Organelles

Phylogenetic Trees

Phylogenetic trees group organisms according to common properties, such as fossils and genomes. Mutations accumulated in genomes serve as a molecular clock.

• Groups of organisms evolved from a common ancestor.

• Each species retains some characteristics of its ancestor.

• Example: The tree shows relationships among Bacteria, Archaea, and Eukarya.

The Taxonomic Hierarchy

The taxonomic hierarchy is a series of subdivisions developed by Linnaeus to classify organisms.

• Hierarchy Levels: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

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

• Mnemonic: "Do Keep Pond Clean Or Froggy Gets Sick" helps remember the order.

Classification of Prokaryotes

Prokaryotic species are defined as populations 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: A catchall kingdom for a variety of organisms; 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: Not part of any domain; not composed of cells; 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 characteristics.

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

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

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

Table: Example of Bacterial Identification Data

Clinical Microbiology Lab Practices

• Lab requisition forms: Used to note types of specimens collected and tests to be conducted.

• Transport media: Used to collect and transport pathogens to a laboratory.

Methods for Identifying Microorganisms

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

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

• Biochemical tests: Determine 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 a number.

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

Additional info: These notes cover the essential concepts of microbial classification, including taxonomy, phylogeny, domain characteristics, and laboratory identification methods, as outlined in a college-level microbiology curriculum.