Classification of Microorganisms

Introduction

The classification of microorganisms is a foundational topic in microbiology, providing a systematic framework for identifying, naming, and grouping organisms based on shared characteristics and evolutionary relationships. This chapter explores the principles and methods used in microbial taxonomy and systematics.

The Study of Phylogenetic Relationships

Taxonomy and Systematics

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

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

Historical Development of Classification Systems

• 1735 (Linnaeus): Established kingdoms Plantae and Animalia.

• 1800s: Bacteria and fungi classified under Plantae (Nägeli); Haeckel proposed Kingdom Protista for bacteria, protozoa, algae, and fungi.

• 1937: The term prokaryote introduced to distinguish cells lacking a nucleus.

• 1968 (Murray): Kingdom Prokaryotae established.

• 1969 (Whittaker): Five-kingdom system proposed.

The Three Domains of Life

Woese's Three-Domain System

• Developed by Carl Woese in 1978, based on rRNA nucleotide sequences.

• Domains:

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

  • Bacteria: True bacteria, prokaryotic.

  • Archaea: Prokaryotes with unique characteristics (e.g., methanogens, extreme halophiles, hyperthermophiles).

Key Concepts of the Three-Domain System

• All organisms evolved from cells that formed over 3 billion years ago.

• DNA passed from ancestors is described as conserved.

• Domain Eukarya includes Fungi, Plantae, Animalia, and protists; Domains Bacteria and Archaea are prokaryotes.

Table: Some Characteristics of Archaea, Bacteria, and Eukarya

Table: Prokaryotic Cells and Eukaryotic Organelles Compared

Origin of Eukaryotes

• Eukaryotes originated from infoldings of prokaryotic plasma membranes.

• Endosymbiotic bacteria developed into organelles (e.g., mitochondria, chloroplasts).

Phylogenetic Trees

• Organisms are grouped according to common properties, such as fossils and genomes.

• Mutations in genomes serve as a molecular clock for evolutionary studies.

• Groups of organisms evolved from a common ancestor, and each species retains some ancestral characteristics.

Scientific Nomenclature

• Common names vary by language and geography, leading to confusion.

• Binomial nomenclature is used worldwide for consistency and accuracy.

• Each organism is given a two-part name: Genus and specific epithet (species).

Table: Making Scientific Names Familiar

The Taxonomic Hierarchy

• Developed by Linnaeus, the hierarchy includes: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

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

Classification of Prokaryotes

• Prokaryotic species: A population 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 diverse kingdom of autotrophic and heterotrophic organisms, grouped into clades based on rRNA.

• Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; reproduce via spores or hyphal fragments.

• Plantae: Multicellular; cellulose cell walls; undergo photosynthesis.

• Animalia: Multicellular; no cell walls; chemoheterotrophic.

Classification of Viruses

• Viruses are not part of any domain; they are not composed of cells and require a host cell for replication.

• Viral species: A 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 known characteristics.

• Identification: Matching characteristics of an unknown organism to 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.

• Clinical microbiology uses lab requisition forms and transport media to collect and transport pathogens.

Laboratory Methods

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

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

• Biochemical tests: Determine the presence of bacterial enzymes.

Metabolic Characteristics and Rapid Identification

• Metabolic characteristics (e.g., fermentation, enzyme production) are used to identify bacteria.

• Rapid identification methods: Perform several biochemical tests simultaneously; results are assigned numbers for identification.

• Automated systems: Use mass spectrophotometry to compare cellular protein spectra to databases.

Serology

• The study of serum and immune responses in serum.

• Microorganisms are antigenic and stimulate antibody production.

• Antiserum: Solution of antibodies tested against unknown bacteria.

• Slide agglutination test: Bacteria agglutinate when mixed with specific antibodies; used to differentiate species and strains.

• ELISA (Enzyme-linked immunosorbent assay): Detects bacteria using known antibodies and color change reactions.

• Western blotting: Identifies antibodies in patient serum; confirms infections such as HIV and Lyme disease.

Phage Typing

• Determines which bacteriophages a bacterium is susceptible to.

• Clearings (plaques) appear on a plate where phages infect and lyse bacterial cells.

Flow Cytometry

• Uses differences in electrical conductivity or fluorescence to distinguish species.

• Fluorescence-activated cell sorting (FACS) is a common application.

DNA Sequencing and Molecular Methods

• DNA base composition: The percentage of guanine + cytosine (GC%) is used to compare relatedness.

• Closely related organisms have similar base compositions.

• Online databases (e.g., NCBI Genome Database) are used for comparison.

DNA Fingerprinting

• Uses electrophoresis of restriction enzyme digests to compare DNA fragments among organisms.

• Provides information on genetic similarities and differences.

Nucleic Acid Hybridization

• Measures the ability of DNA strands from different organisms to hybridize.

• A high degree of hybridization (≥70%) indicates the same species.

• Nucleic Acid Amplification Tests (NAAT): Use PCR to amplify DNA of unculturable microorganisms.

• Southern blotting: Uses DNA probes to identify unknown microorganisms.

• DNA chips (microarrays): Contain DNA probes to detect pathogens by hybridization and fluorescence.

• Ribotyping: Uses rRNA sequencing for identification.

• Fluorescent in situ hybridization (FISH): Uses fluorescent probes to stain and identify microorganisms in samples.

Integrating Classification Methods

• Dichotomous keys: Identification tools based on a series of questions with two possible answers.

• Cladograms: Diagrams that show evolutionary relationships based on rRNA sequences.