Microbial Taxonomy, Classification, and Identification: Study Guide

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Taxonomy and Classification

Definition and Purpose of Taxonomy

Taxonomy is the science of classifying organisms. It organizes microorganisms based on shared characteristics and evolutionary relationships, providing universal scientific names and aiding in the identification of unknown organisms.

Taxonomy: The systematic classification of organisms.
Purposes:
- Shows relationships among organisms.
- Provides universal scientific names to prevent confusion.
- Helps identify unknown organisms.
Systematics (Phylogeny): Studies evolutionary history and relationships among organisms, often using phylogenetic trees.

Example: Humans and chimpanzees are different species but share a common ancestor; similarly, bacteria and other microorganisms are classified based on evolutionary evidence.

Historical Development of Classification Systems

Classification systems have evolved as scientific knowledge advanced, moving from simple observable traits to molecular and genetic evidence.

Year	Change	Reason
1735	Plants vs. Animals	Classification based on visible traits
1857	Bacteria & Fungi added to plants	Nonmoving organisms thought to be plants
1866	Kingdom Protista created	Microorganisms didn't fit into only two kingdoms
1937	Prokaryote introduced	Recognition of cells without a nucleus
1959	Kingdom Fungi created	Fungi recognized as fundamentally different from plants
1968	Kingdom Monera (Prokaryotae) proposed	Grouping all prokaryotes together
1978	Bacteria and Archaea distinguished	Molecular evidence revealed two distinct prokaryotic groups

Additional info: Each change was driven by new scientific discoveries, especially advances in microscopy and molecular biology.

Modern Classification: The Three-Domain System

Three Domains of Life

The Three-Domain System, proposed by Carl Woese, is based on ribosomal RNA (rRNA) sequencing and divides life into three domains:

Bacteria: Prokaryotic, "true bacteria," cell wall contains peptidoglycan, circular DNA, 70S ribosomes, binary fission.
Archaea: Prokaryotic, genetically closer to Eukarya, no peptidoglycan, unique cell wall materials, circular DNA, 70S ribosomes, binary fission, have histones.
Eukarya: Eukaryotic cells, true nucleus, linear DNA, histones, 80S ribosomes, mitosis.

Key Point: Archaea are genetically more closely related to Eukarya than to Bacteria, despite both being prokaryotes.

Characteristics of Domains

Feature	Bacteria	Archaea	Eukarya
Nucleus	No	No	Yes
DNA	Circular	Circular	Linear
Histones	No	Yes	Yes
Ribosomes	70S	70S	80S
Cell Wall	Peptidoglycan	No peptidoglycan	Varies
Division	Binary fission	Binary fission	Mitosis

Taxonomic Hierarchy and Species Definitions

Taxonomic Hierarchy

The taxonomic hierarchy organizes organisms from broadest to most specific:

Domain (broadest)
Kingdom
Phylum
Class
Order
Family
Genus
Species (most specific)

As you move down the hierarchy, organisms become more similar and share more characteristics.

Species Definitions

Eukaryotic species: Group of closely related organisms that breed among themselves.
Prokaryotic species: Population of cells with similar characteristics.
Clone: Population of cells derived from a single cell.
Strain: Genetically different cells within a clone.
Viral species: Population of viruses with similar characteristics occupying a particular ecological niche.

Example: Escherichia coli O157:H7 is a pathogenic strain of E. coli.

Scientific Nomenclature

Binomial Naming System

Each organism receives a two-part scientific name: Genus and Species. Names are governed by international committees and often reflect the discoverer or key characteristics.

Klebsiella pneumoniae: Named after Edwin Klebs; causes pneumonia.
Streptococcus pyogenes: Chain-forming spherical bacterium that produces pus.
Penicillium notatum: Brush-like fungus; widely dispersed spores.

Key Point: Scientific names are universal and often descriptive.

Identification Methods in Microbiology

Workflow for Identifying Unknown Microorganisms

Microbiologists use a stepwise approach to identify unknown bacteria:

Observe morphology (shape, arrangement).
Perform differential staining (Gram stain, acid-fast stain).
Conduct biochemical tests (enzyme activity, fermentation, catalase, citrate).
Compare results with identification references (e.g., Bergey's Manual).

Key Point: Identification requires multiple tests; no single test is sufficient.

Identification Methods

Morphology: Shape (coccus, bacillus, spirillum), arrangement (chains, clusters).
Differential staining: Gram stain separates bacteria into two groups; acid-fast stain identifies mycobacteria.
Biochemical tests: Detect enzyme activity and metabolic capabilities.

Numerical Identification

Numerical identification uses the combined results of multiple laboratory tests to identify bacteria. Each additional test narrows the possible identities.

Dichotomous Key

A dichotomous key is a step-by-step tool using a series of two-choice questions to identify organisms.

Each question has two possible answers (e.g., Gram-positive or Gram-negative).
Each answer directs you to the next question, eliminating possibilities.

Serological Identification Methods

Serology and Antigen-Antibody Reactions

Serology identifies microorganisms using antigen-antibody specificity. Antibodies bind only to their matching antigens, allowing precise identification.

Antigen: Molecule on a microorganism's surface that stimulates an immune response.
Antibody: Protein produced by B cells that binds specifically to its matching antigen.

Serological Methods

Method	Positive Result	Key Feature
Agglutination	Clumping	Antibodies cross-link cells
Fluorescent antibody	Cells glow	Antibody carries fluorescent dye
ELISA	Color change	Antibody carries an enzyme

Agglutination: Antibodies bind to antigens on multiple microorganisms, causing visible clumping.
Fluorescent antibody test: Antibody is labeled with a fluorescent dye; binding causes cells to glow under a fluorescence microscope.
ELISA (Enzyme-Linked Immunosorbent Assay): Antibody is linked to an enzyme; binding and substrate addition produce a color change.

Western blot: Detects specific proteins using antibodies; produces visible protein bands and is used as a confirmatory test.

Other Identification Methods

Phage Typing

Phage typing uses bacteriophages to identify bacteria based on susceptibility to viral infection. If a phage infects and lyses the bacterium, a clear zone (plaque) forms.

Flow Cytometry

Flow cytometry is an automated method where cells pass through a laser beam one at a time. It measures cell size (forward scatter), internal complexity (side scatter), and fluorescence (if fluorescent antibodies are used).

Rapid, automated identification.
Can analyze thousands of cells per second.
Fluorescent antibodies detect specific antigens.

Nucleic Acid Hybridization

Nucleic acid hybridization compares DNA or RNA sequences to determine genetic similarity. Complementary strands pair together; more hybridization indicates closer relatedness.

DNA must be separated into single strands.
Degree of hybridization reflects genetic similarity.

Cladograms and Phylogenetic Trees

Cladograms (Phylogenetic Trees)

Cladograms are branching diagrams showing evolutionary relationships among organisms based on shared characteristics or genetic information.

Root: Represents the universal ancestor.
Node: Branching point representing a shared common ancestor.
Branch: Represents an evolutionary lineage.
Closer branches indicate more closely related organisms.

Key Point: Modern cladograms often use DNA and rRNA sequence data.

Domain Eukarya: The Four Kingdoms

Kingdoms and Their Characteristics

Kingdom	Cell Wall	Nutrition	Cellularity
Animalia	None	Chemoheterotrophic	Multicellular
Plantae	Cellulose	Photoautotrophic	Multicellular
Fungi	Chitin	Chemoheterotrophic	Unicellular or multicellular
Protista	Varies	Varies	Mostly unicellular

Animalia: Multicellular, no cell walls, chemoheterotrophic.
Plantae: Multicellular, cellulose cell walls, photoautotrophic.
Fungi: Unicellular or multicellular, chitin cell walls, chemoheterotrophic.
Protista: Diverse group; includes protozoa, algae, slime molds.

Domain Archaea: Major Groups

Three Major Groups of Archaea

Methanogens: Produce methane gas; found in anaerobic environments (swamps, digestive tracts).
Extreme Halophiles: Thrive in high-salt environments (Dead Sea, salt ponds).
Hyperthermophiles: Grow at very high temperatures (hot springs, hydrothermal vents).

Key Point: Archaea demonstrate life's adaptability to extreme environments and are important for biotechnology.

Endosymbiotic Theory

Origin of Mitochondria and Chloroplasts

The Endosymbiotic Theory proposes that mitochondria and chloroplasts originated from bacteria engulfed by ancestral eukaryotic cells. These organelles retain bacterial characteristics:

Circular DNA
No histones
70S ribosomes
Binary fission

Example: Mitochondria evolved from aerobic bacteria; chloroplasts from photosynthetic cyanobacteria.

References for Microbial Identification

Bergey's Manuals and Approved Lists

Bergey's Manual of Determinative Bacteriology: Used for laboratory identification based on morphology, staining, and biochemical tests.
Bergey's Manual of Systematic Bacteriology: Focuses on classification and evolutionary relationships using rRNA sequencing.
Approved Lists of Bacterial Names: Official record of accepted bacterial names based on published research.

Key Point: Laboratories use standardized references for identification and classification.

Summary Table: Identification Methods

Method	Purpose	Key Feature
Morphology	Physical appearance	Shape, arrangement
Differential staining	Cell wall properties	Gram stain, acid-fast stain
Biochemical tests	Enzyme activity	Fermentation, catalase, citrate
Serology	Antigen-antibody reactions	Agglutination, fluorescent antibody, ELISA
Phage typing	Viral susceptibility	Bacteriophage lysis
Flow cytometry	Automated cell analysis	Laser, scatter, fluorescence
Nucleic acid hybridization	Genetic similarity	DNA/RNA pairing

Key Takeaways

Taxonomy organizes and identifies microorganisms based on shared characteristics and evolutionary relationships.
The Three-Domain System is based on molecular evidence, especially rRNA sequencing.
Identification of microorganisms requires multiple tests and standardized references.
Modern classification emphasizes genetic and molecular data over simple observable traits.