Concepts and Tools for Studying Microorganisms

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