Chapter 3
Concepts and Tools for Studying Microorganisms
3.1 The Prokaryotic/Eukaryotic Paradigm
 Prokaryote/Eukaryote Similarities
• Homeostasis is an organism’s ability to maintain a stable internal state
• Many prokaryotes live in communal associations called biofilms
• Myxobacteria live in a social community dependent on cell-to-cell
interaction and communication
• Prokaryotes carry out many of the same cellular processes as eukaryotes
 Prokaryotes and Eukaryotes: The Similarities in Organizational Patterns
• All organisms have similar genetic organization whereby heredity material
is expressed
• Both prokaryotic and eukaryotic cells have internal compartments
• Metabolism occurs in the cytoplasm
• Ribosomes are involved in protein synthesis
 Prokaryotes and Eukaryotes: The Structural Distinctions
• Eukaryotes have membrane-enclosed organelles
• Protein/lipid transport in eukaryotes is carried out by the endoplasmic
reticulum and Golgi apparatus
• Mitochondria perform cellular respiration in eukaryotes
• Both eukaryotes and prokaryotes can perform photosynthesis
 Prokaryotes and Eukaryotes: The Structural Distinctions
• The eukaryotic cytoskeleton gives the cell structure and transports
materials within the cell
• Both eukaryotes and prokaryotes use flagella for motility, though the
flagella differ structurally and functionally in the two groups
• Many prokaryotes and eukaryotes have a cell wall to help maintain water
balance
3.2 Cataloging Microorganisms
 Classification Attempts to Catalog Organisms
• Taxonomy is the science of classification, involving arranging related
organisms into logical categories
• In the mid-1700s, Carolus Linnaeus published Systema Naturae,
establishing a uniform system for naming organisms
 Nomenclature Gives Scientific Names to Organisms
• Each name includes two words, the genus and the specific epithet
 Classification Uses a Hierarchical System
• The levels of classification are species, genus, family, order, class,
phylum/division, kingdom, and domain
 Kingdoms and Domains: Trying to Make Sense of Taxonomic Relationships
• In 1886, Ernst H. Haeckel coined the term “protist” for all microorganisms
• Robert H. Whittaker and Lynn Margulis developed the five-kingdom
system, giving bacteria their own kingdom
 The Three-Domain System Places the Prokaryotes in Separate Lineages
• The three-domain system was proposed by Carl Woese, based on data
from ribosomal RNA sequences
• The three-domain system includes Bacteria, Eukarya, and Archaea
 Distinguishing Between Prokaryotes
• Experiments on physical characteristics, biochemistry, serology
(antibodies), and nucleic acids can be done to identify microbes
• Molecular taxonomy is bases on sequences of nucleic acids in ribosomal
RNA
• The dichotomous key can be used identify microbes
3.3 Microscopy
 Most Microbial Agents Are in the Micrometer Size Range
• Most bacterial and archaeal cells are 1–5 micrometers (µm) in length
 Light Microscopy Is Used to Observe Most Microorganisms
• Visible light passes through multiple lenses and through the specimen
• Light microscopes usually have at least 3 lenses: low-power, high-power,
and oil-immersion
• The lens system must have high resolving power to see the specimen
clearly
 Staining Techniques Provide Contrast
• The simple stain technique involves flooding a prepared specimen with
basic dye
• The negative stain technique uses acidic dye, which is repelled by cell
walls, leaving clear cells on a dark background
• In the Gram stain technique, cells are stained with crystal violet and
Gram’s iodine solution and washed with a decolorizer
• Gram-positive bacteria retain the crystal violet, whereas gram-negative
bacteria do not
• Mycobacteria can be stained with carbol-fuchsin in the acid-fast technique
 Light Microscopy Has Other Optical Configurations
• Phase-contrast microscopy a special condenser and objective lenses to
allow observers to view living, unstained organisms
• Dark-field microscopy shows the specimen against a dark background and
provides good resolution
• In fluorescence microscopy, specimens are coated with fluorescent dye
and illuminated with ultraviolet light
 Electron Microscopy Provides Detailed Images of Cells, Cell Parts, and Viruses
• Electrons are absorbed, deflected, or transmitted based on the density of
structures in the specimen
• The practical limit of an electron microscope’s resolution is about 2 nm
• The transmission electron microscope visualizes structures in ultrathin
section of cells
• The scanning electron microscope is used to visualize surfaces of
unsectioned objects