Brock Biology of Microorganisms - In Depth Notes

A Brief Journey to the Microbial World

I. Seeing the Very Small

2.1 Some Principles of Light Microscopy
  • Compound Light Microscope: Utilizes visible light to illuminate cells.
  • Types of Light Microscopy:
    • Bright-field
    • Phase-contrast
    • Dark-field
    • Fluorescence
Bright-field Microscopy
  • Specimens are visualized based on contrast differences (density) between the specimen and surroundings.
  • Two lens systems create the image:
    • Objective Lens
    • Ocular Lens
  • Total Magnification: extTotalMagnification=extObjectiveMagnificationimesextOcularMagnificationext{Total Magnification} = ext{Objective Magnification} imes ext{Ocular Magnification}
  • Maximum magnification is approximately 2000x.
2.1 Some Principles of Light Microscopy (Cont'd)
  • Resolution: Ability to distinguish two adjacent objects as separate; determined by light wavelength and numerical aperture of lens.
  • Limit of Resolution for Light Microscope: about 0.2 μm.
2.2 Improving Contrast in Light Microscopy
  • Staining: Enhances contrast for clearer images.
  • Dyes bind to specific cellular materials, with common stains including methylene blue, safranin, and crystal violet.
Differential Stains
  • Gram Stain: Distinguishes bacteria into two major groups: gram-positive (purple) and gram-negative (red).
Other Techniques to Improve Contrast
  • Phase-Contrast Microscopy: Enhances contrast without staining, visualizes live samples.
  • Dark-Field Microscopy: Illumination from the side creates a light specimen on a dark background.
  • Fluorescence Microscopy: Visualizes fluoroscent specimens, useful in microbial ecology.

II. Imaging Cells in Three Dimensions

2.3 Techniques for 3D Imaging
  • Differential Interference Contrast (DIC) Microscopy: Uses polarized light for a 3D effect.
  • Atomic Force Microscopy (AFM): Measures repulsive forces for imaging.
  • Confocal Scanning Laser Microscopy (CSLM): Uses lasers to compile images from different layers with a resolution of 0.1 μm.

III. Electron Microscopy

2.4 Types of Electron Microscopy
  • Transmission Electron Microscopy (TEM):
    • High magnification and resolution (0.2 nm).
    • Requires specimens to be thin (20–60 nm) and stained.
  • Scanning Electron Microscopy (SEM):
    • Coats specimens with heavy metal, captures scattered electrons, magnification between 15x and 100,000x.

IV. Cell Structure and Evolutionary History

2.5 Elements of Microbial Structure
  • All cells share:
    • Cytoplasmic Membrane
    • Cytoplasm
    • Ribosomes
2.6 DNA Arrangement in Microbial Cells
  • Prokaryotic Genome: Typically a single, circular DNA molecule; may include plasmids providing special traits (e.g., antibiotic resistance).
  • Eukaryotic DNA: Linear, found in the nucleus, associated with proteins, typically two copies per chromosome.
2.7 The Evolutionary Tree of Life
  • Phylogeny: The study of evolutionary relationships, established through genetic information.
  • Domains Identified:
    • Bacteria
    • Archaea
    • Eukarya
    • Not closely related; Archaea are more related to Eukarya than Bacteria.

V. Microbial Diversity

2.8 Metabolic Diversity
  • Microbial Diversity: Result of around 4 billion years of evolution across size, shape, physiology, etc.
  • Nutrition Classification:
    • Chemoorganotrophs: Energy from organic molecules.
    • Chemolithotrophs: Energy from inorganic molecules.
    • Phototrophs: Use light energy; includes oxygen production or not.
2.9 Bacteria
  • Includes significant pathogens; the dominant phylum is Proteobacteria (e.g., E. coli, Salmonella).
2.10 Archaea
  • Two primary phyla:
    • Euryarchaeota: Methanogens and extremophiles.
    • Crenarchaeota: Hyperthermophiles.
2.11 Phylogenetic Analyses
  • Much microbial diversity remains uncultured. Use of molecular techniques reveals more complexity than traditional methods.
2.12 Microbial Eukarya
  • Includes algae, fungi, slime molds, etc.
  • Lichens: Mutualistic associations between fungi and cyanobacteria or algae.