Brock Biology of Microorganisms: The Microbial World (Chapter 1) - Study Notes

The Microbial World

Introduction to Microorganisms

Microorganisms, or microbes, are life forms too small to be seen by the human eye and require a microscope for observation. They are classified into prokaryotic (before nucleus), eukaryotic (true nucleus), and viruses (not free-living cells, require a host for reproduction).

• Prokaryotic microbes: Include Bacteria (e.g., Streptococcus pyogenes), Cyanobacteria (e.g., Anabeana), and Archaea (e.g., Methanocaldococcus jannaschii).

• Eukaryotic microbes: Include fungi (e.g., Candida albicans, Rhizopus stolonifer), protists (e.g., Trypansoma cruzi), animals (e.g., Trichuris vulpis), and plants (e.g., Spirogyra).

• Viruses: Non-cellular entities composed of DNA or RNA surrounded by a protein coat, sometimes with an envelope. They require host cells to replicate.

Microorganisms: Importance and Applications

Microorganisms are the oldest form of life, constitute a major fraction of Earth's biomass, and have profound effects on human life, including infectious diseases, food and water safety, soil fertility, animal health, and fuel production. Pathogens are organisms that cause diseases.

Studying Microbes: Tools and Techniques

Microscopy and Culture Media

Microbes are studied using microscopes (compound light and electron microscopes) and culture media. Culture media can be liquid (broth), solid (agar), or slanted. Growth refers to an increase in cell number due to cell division, and a colony is a visible mass containing millions or billions of cells.

• Plated media: Trypticase Soy Agar (TSA), Mannitol Salt Agar (MSA)

• Liquid media: Trypticase Soy Broth (TSB), Glucose purple broth

• Slanted media: TSA slants, Citrate Agar Slants

Structure and Activities of Microbial Cells

Basic Cell Structure

All cells share common structural elements:

• Cytoplasmic (cell) membrane: Phospholipid bilayer that separates the cytoplasm from the external environment.

• Cytoplasm: Aqueous mixture of macromolecules, small organics, ions, and ribosomes.

• Ribosomes: Protein-synthesizing structures; bacteria have 70S ribosomes, eukaryotes have 80S ribosomes.

Cell Walls

• Bacteria: Peptidoglycan (murein)

• Acid-fast bacteria: Mycolic acids in cell walls

• Archaea: Pseudopeptidoglycan (pseudomurein)

• Fungi: Chitin

• Plants: Cellulose

• Animal cells: No cell walls, only cell membranes; sensitive to osmotic pressure

• Mycoplasma: Bacteria without cell walls, pleomorphic, causes walking pneumonia

Genetic Material and Genome Organization

• Genome: Full set of genes in a cell

• Eukaryotic DNA: Linear chromosomes within a nucleus, large genome

• Prokaryotic DNA: Single circular chromosome in nucleoid region, may have plasmids (antibiotic resistance), small and compact genome

Cell Activities

• Metabolism: Chemical transformation of nutrients; includes aerobic, anaerobic, and facultative anaerobic processes

• Enzymes: Protein catalysts for biochemical reactions

• Transcription: DNA to RNA

• Translation: RNA to protein

• DNA replication: Copying the genome

• Motility: Movement via flagella (bacteria) or cilia/flagella (eukaryotes)

• Differentiation: Formation of specialized cells (endospores in bacteria, spores in fungi, pili for conjugation)

• Intercellular communication: Chemical signaling (quorum sensing)

• Evolution: Genetic changes passed to offspring

Cell Size and Morphology

Cell Size Range

Cell size and shape (morphology) vary widely among microbes. Prokaryotes range from 0.2 µm to 600+ µm in diameter, most between 0.5 and 10 µm. Eukaryotic cells are typically 5 to 100 µm in length.

Organism	Size (µm)	Morphology	Characteristics
Thiomargarita namibiensis	750	Cocci in chains	Sulfur chemolithotroph
Epulopiscium fishelsonia	80 × 600	Rods with tapered ends	Chemoorganotroph
Escherichia coli	1 × 2	Rods	Chemoorganotroph
Mycoplasma pneumoniae	0.2	Pleomorphic	Pathogenic bacterium

Introduction to Microbial Life

Three Domains of Life

All cellular life is classified into three domains: Bacteria, Archaea, and Eukarya.

• Bacteria: Prokaryotes, usually undifferentiated single cells, 0.5–10 μm long, e.g., E. coli (rod-shaped), Staphylococcus aureus (cocci-shaped)

• Archaea: Prokaryotes, often extremophiles, no known parasites or pathogens of plants and animals

• Eukarya: Includes plants, animals, fungi, protists; first were unicellular, may have appeared two billion years ago; endosymbiotic theory explains origin of mitochondria and chloroplasts

Viruses

• Obligate parasites, replicate only within host cells

• Not cells, do not carry out metabolism

• Small genomes of double- or single-stranded DNA or RNA

• Classified by structure, genome composition, and host specificity

Microorganisms and the Biosphere

History of Life on Earth

Earth is 4.6 billion years old. First cells appeared between 3.8 and 4.3 billion years ago. The atmosphere was anoxic until ~2.6 billion years ago, supporting only anaerobic metabolisms. Cyanobacteria (oxygenic phototrophs) appeared ~2.6 billion years ago, and plants and animals ~0.5 billion years ago.

Microbial Ecology and Extremophiles

Microbial ecology studies how microbes affect animals, plants, and ecosystems. Extremophiles live in habitats too harsh for other life forms, such as hot springs, glaciers, high salt, acidity/alkalinity, and pressure.

Descriptive Term	Habitat	Domain	Genus, Species	Extreme Condition
Hyperthermophile	Undersea hydrothermal vents	Archaea	Methanopyrus kandleri	High temperature (up to 122°C)
Psychrophile	Sea ice	Bacteria	Psychromonas ingrahamii	Low temperature (-12°C)
Acidophile	Acidic hot springs	Archaea	Picrophilus oshimae	Low pH (0.7)
Halophile	Salterns	Archaea	Halobacterium salinarum	High salt (32% NaCl)

Impact of Microorganisms on Human Society

Microorganisms as Disease Agents

Microorganisms can be both beneficial and harmful. Pathogens cause disease, but most microbes are beneficial, contributing to vaccination, antibiotic therapy, water treatment, and food safety.

Microorganisms in Agriculture and Nutrition

• Nitrogen-fixing bacteria: Convert atmospheric nitrogen to ammonia for plant use

• Cellulose-degrading microbes: In the rumen of cattle, help digest plant matter

• Gut microbiome: Digests complex carbohydrates in humans, synthesizes vitamins and nutrients

Microorganisms and Food

• Negative impacts: Food spoilage and foodborne disease

• Positive impacts: Food safety and preservation, production of dairy products (cheese, yogurt), fermented foods (sauerkraut, kimchi, pickles, chocolate, coffee, bread, alcohol)

Microorganisms and Industry

• Industrial microbiology: Use of microbes in pharmaceuticals, brewing, and biotechnology

• Biotechnology: Genetically engineered microbes produce high-value products

• Biofuels: Production of methane and ethanol

• Wastewater treatment and bioremediation: Cleaning up pollutants

• Biofilms: Growth on submerged surfaces (pipes, drains, medical devices)

Microscopy and Discovery of Microorganisms

History of Microscopy

Microbiology began with the invention of the microscope. Robert Hooke first described microbes in 1665, and Antonie van Leeuwenhoek was the first to see bacteria.

Types of Light Microscopy

• Bright-field: Visualizes specimens by differences in contrast

• Phase-contrast: Amplifies differences in refractive index

• Differential interference contrast: Enhances contrast in unstained cells

• Dark-field: Light scattered by specimen, excellent for motility observation

• Fluorescence: Visualizes specimens that fluoresce, widely used in diagnostics

Staining Techniques

• Simple stains: Use basic dyes (methylene blue, crystal violet, safranin) to increase contrast

• Negative stains: Stain the background, not the cell (Nigrosin, India ink, Congo Red)

• Differential stains: Render different cells different colors; Gram stain distinguishes gram-positive (purple-violet) and gram-negative (red/pink) bacteria

Advanced Microscopy

• Confocal scanning laser microscopy (CSLM): Generates three-dimensional images using a laser and computer

• Electron microscopy: Uses electrons instead of light; includes transmission electron microscopes (TEM, see inside cells) and scanning electron microscopes (SEM, see cell surfaces)

Microbial Cultivation and Historical Experiments

Aseptic Technique and Pure Cultures

• Aseptic technique: Practices to maintain sterile media and solutions

• Pure cultures: Cells from a single type of microorganism

• Enrichment culture techniques: Isolate microbes with specific metabolic characteristics

Pasteur and Spontaneous Generation

Louis Pasteur disproved the theory of spontaneous generation using the swan-necked flask experiment, leading to sterilization methods and food preservation. He also developed vaccines for anthrax, fowl cholera, and rabies.

Koch and Infectious Disease

Robert Koch demonstrated the link between microbes and infectious diseases (germ theory), identified causative agents of anthrax, tuberculosis, and cholera, and developed Koch's postulates to link cause and effect in infectious disease. He also developed solid media for pure cultures.

Molecular Basis of Life and Evolution

Foundations of Molecular Biology

• Rapid growth of bacteria under controlled conditions makes them excellent models for studying molecular biology, genetics, and biochemistry.

• Genetic transfer in bacteria and the discovery that DNA is the genetic material were foundational (Griffith, Avery-MacLeod-McCarty, Watson, Crick, Franklin).

Woese and the Tree of Life

• Ribosomal RNA (rRNA) sequencing enabled the construction of the phylogenetic tree of life, showing three domains: Bacteria, Archaea, and Eukarya.

• LUCA (last universal common ancestor) is the root of the tree.

• Most microbes have not been cultured yet; DNA sequencing technology allows study of entire genomes.