Chapter 3 Concepts and Tools for Studying Microorganisms

Chapter 3 Concepts and Tools for Studying Microorganisms

3. 1 The Prokaryotes Are Not Simple, Primitive Organisms Figure 03. 02 A: Staphylococcus aureus. © SPL/Photo Researchers, Inc. § Prokaryote/Eukaryote Similarities • DNA is the hereditary material that controls structure and function • Biochemical reactions are used for growth and energy conversions • Response to stimuli • Reproduce to produce offspring • Adapt from one generation to the next • Interactions with other organisms and their environment

All living organisms share the common properties of life § Homeostasis maintains a stable internal environment § Biofilms interact through a multicellular association • Quorum sensing is a chemical communication and cooperation between cells Figure 03. 03 AB: Cell Communication and Quorum Sensing.

Bacterial and Eukaryotic Cells Share Organizational Patterns • • Genetic organization with DNA in Chromosomes Compartmentation with cell membranes Metabolic organization in the cytoplasm Protein synthesis at ribosomes Figure 03. 05 AB: A Comparison of a Bacterial and Eukaryotic Cell.

Bacterial Complexity: Bacterial cells have processes as complex as in eukaryotes. Figure 03. 02 C: Biofilm. Figure 03. 02 B: Homeostasis concept map. Modified from David G. Davies, Binghamton University, Binghamton NY

Prokaryotes and Eukaryotes: The Similarities in Organizational Patterns § Cell theory: the cell is the fundamental unit of life. § Hereditary information is organized in chromosomes. § Cytoplasm is surrounded by a cell membrane which selectively allows substances in or out of the cell. § Metabolism is the chemical reactions that occur in the cell. § Protein synthesis occurs at the ribosome. Figure 03. 01 Prochlorococcus. © Claire Ting/Photo Researchers, Inc.

Prokaryotes and Eukaryotes: The Structural Distinctions • Eukaryotes have membraneenclosed organelles, some bacteria have microcompartments surrounded by protein. • Protein/lipid transport in eukaryotes is carried out by the endoplasmic reticulum and Golgi apparatus. • Mitochondria perform cellular respiration in eukaryotes, while prokaryotes use the cytoplasm and cell membrane. • Both eukaryotes and prokaryotes can perform photosynthesis. Figure 03. 05 B: Eukaryote cells.

• 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 by osmosis. Table 03. 01: Comparison of Prokaryotic and Eukaryotic Cell Structure.

Similarities Between Mitochondria, Chloroplasts, Bacterial and Microbial Eukaryotes Microinquiry 3 Evolution of Eukaryotic Cells Figure A. 9

3. 2 Classifying Microorganisms Reveals Relationships Between Organisms § Classification attempts to catalog organisms. • Taxonomy is the science of classification, arranging related organisms into categories. § Classification uses a hierarchical system. Table 03. 02: Taxonomic Classification.

Nomenclature gives scientific names to organisms. • In the mid-1700 s, Carolus Linnaeus published Systema Naturae, establishing a uniform system for naming organisms. • Each name includes two words, the genus and the specific epithet that together make up the species name. o Ex) Escherichia coli

§ 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 in 1959 developed the fivekingdom system, giving bacteria their own kingdom. • Plantae • Animalia • Protista • Fungi • Bacteria

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. Figure 03. 07: The Three-Domain System Forms the “Tree of Life”.

Many methods are available to identify and classify microorganisms. • In 1984, Bergey’s Manual of Systematic Bacteriology • 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. Figure 03. 08: Micro. Scan panel. Courtesy of Biolog

The dichotomous key can be used identify microbes. Microfocus 03. 03 Tools Dichotomous Key Flow Chart.

3. 3 Microscopy Is Used to Visualize the Structure of Cells Most microbial agents are in the micrometer size range. • Most bacterial and archaeal cells are 1– 5 micrometers (µm) in length. Figure 03. 09: Size comparisons among various atoms, molecules, and microorganisms.

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, highpower, and oil-immersion. • The lens system must have high resolving power to see the specimen clearly. Figure 03. 10 B: Light microscope.

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. Figure 13. 11 AB: Important staining reactions in microbiology.

• In the Gram stain technique, cells are stained with crystal violet and Gram’s iodine solution and washed with a decolorizer. • Safranin is applied as a counter stain. • Gram-positive bacteria retain the crystal violet, whereas gram-negative bacteria do not. Figure 03. 11 C: Important Staining Reactions in Microbiology.

• Mycobacteria can be stained with carbol-fuchsin in the acid-fast technique. • The red cells are acid-fast as seen in TB. Figure 03. 12 D: Acid-Fast Stain Mycobacterium tuberculosis. Courtesy of Jeffrey Pommerville

Figure 03. 13 A Phase Contrast. Courtesy of Larry Stauffer, Oregon State Public Health Laboratory/CDC • Phase-contrast microscopy a special condenser and objective lenses allow observers to view living, unstained organisms. • Dark-field microscopy shows the specimen against a dark background and provides good resolution. Courtesy of Schwartz/CDC § Light microscopy has other optical configurations. Figure 13. 13 B: Dark Field.

• In fluorescence microscopy, specimens are coated with fluorescent dye and illuminated with ultraviolet light. Figure 03. 14: Fluorescence Antibody Technique.

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. Figure 03. 15: the Electron Microscope. Courtesy of Carl Zeiss Microscopy

• The transmission electron microscope visualizes structures in ultrathin section of cells. Figure 03. 16 A: Psedomonas whole cells TEM. © CNRI/Photo Researchers, Inc.

• The scanning electron microscope is used to visualize surfaces of unsectioned objects. Figure 03. 16 B: Psedomonas whole cells SEM. © Dr. Dennis Kunkel/Visuals Unlimited