Chapter 11: Classification and Diversity of Prokaryotes

Gram-Positive Bacteria: Phyla and G+C Content

• Firmicutes: Characterized by a low G+C content in their DNA. Includes genera such as Bacillus, Clostridium, Staphylococcus, and Streptococcus.

• Actinobacteria: Characterized by a high G+C content. Includes Mycobacterium, Corynebacterium, Streptomyces, and others.

• G+C Content: Refers to the proportion of guanine (G) and cytosine (C) bases in the DNA. High G+C content often correlates with certain physiological and structural traits.

Proteobacteria: Major Phylum of Gram-Negative Bacteria

• Proteobacteria: A large and diverse phylum of Gram-negative bacteria, divided into classes such as Alpha-, Beta-, and Gammaproteobacteria.

• Alphaproteobacteria:

  • Rickettsia: Obligate intracellular parasites, transmitted by arthropod vectors (e.g., ticks). Cause diseases such as typhus and Rocky Mountain spotted fever.

  • Bartonella: Causes cat scratch disease.

  • Brucella: Causes brucellosis, a zoonotic infection.

  • Rhizobium: Involved in nitrogen fixation in plant root nodules.

• Betaproteobacteria:

  • Bordetella: Causes whooping cough (B. pertussis).

  • Neisseria: Includes species causing gonorrhea (N. gonorrhoeae) and meningitis (N. meningitidis).

• Gammaproteobacteria:

  • Pseudomonadales: Pseudomonas—opportunistic pathogens, highly resistant to antibiotics.

  • Legionellales: Legionella—causes Legionnaires’ disease, often associated with water systems.

  • Vibrionales: Vibrio—causes cholera.

  • Enterobacteriales (Enterics):

    • Common traits: Gram-negative rods, facultative anaerobes, ferment glucose, reduce nitrate.

    • Escherichia: Gut flora, can cause infections.

    • Enterobacter: Opportunistic infections, especially UTIs.

    • Salmonella: Food poisoning.

    • Shigella: Dysentery.

    • Klebsiella: Pneumonia, found in water and soil.

    • Serratia: Opportunistic infections (Additional info: often produces red pigment).

    • Proteus: Urinary tract infections, highly motile (Additional info: swarming motility).

    • Yersinia: Plague (Y. pestis).

• Epsilonproteobacteria:

  • Campylobacter: Food poisoning, especially from undercooked poultry.

  • Helicobacter: Causes stomach ulcers, linked to gastric cancer.

Chlamydiae vs. Rickettsias

• Chlamydiae: Obligate intracellular bacteria, lack peptidoglycan in cell wall, unique biphasic life cycle, no arthropod vectors. Cause chlamydia (sexually transmitted infection) and trachoma (eye infection).

• Rickettsias: Also obligate intracellular, but transmitted by arthropod vectors (e.g., ticks, lice), have peptidoglycan.

Spirochaetes: Unique Features and Diseases

• Spirochaetes: Spiral-shaped, flexible bacteria with axial filaments (endoflagella) for motility.

• Treponema: Causes syphilis (T. pallidum).

• Borrelia: Causes Lyme disease.

• Leptospira: Causes leptospirosis, a zoonotic disease.

Phylum Firmicutes: Key Genera and Diseases

• Clostridiales:

  • Clostridium: Anaerobic, spore-forming rods. Diseases: tetanus, botulism, gas gangrene, and C. difficile infections.

• Bacillales:

  • Bacillus: Causes anthrax (B. anthracis).

  • Staphylococcus: Causes skin infections, food poisoning (S. aureus).

• Lactobacillales:

  • Lactobacillus: Used in yogurt and probiotics.

  • Streptococcus: Differentiated by hemolysis on blood agar:

    • Beta-hemolytic: Complete lysis of red blood cells (clear zone).

    • S. pyogenes: Strep throat.

    • S. pneumoniae: Pneumonia.

    • S. mutans: Dental caries (tooth decay).

  • Enterococcus: Opportunistic infections, especially in hospitals.

  • Listeria: Causes listeriosis, can grow at refrigeration temperatures.

• Mycoplasma: Lack a cell wall, making them resistant to penicillin and other beta-lactam antibiotics. Cause atypical pneumonia.

Phylum Actinobacteria: Key Genera and Features

• Mycobacterium: Acid-fast, causes tuberculosis and leprosy.

• Corynebacterium: Causes diphtheria.

• Propionibacterium: Causes acne (P. acnes).

• Streptomyces: Produces many antibiotics (e.g., streptomycin).

• Actinomyces: Causes oral infections; many form branching filaments resembling fungi.

Chapter 6: Microbial Growth

Temperature and Microbial Growth

• Minimum Temperature: Lowest temperature at which growth occurs; enzyme activity is very slow.

• Optimum Temperature: Temperature at which growth rate is highest; enzymes function most efficiently.

• Maximum Temperature: Highest temperature at which growth is possible; enzymes denature above this point.

• Temperature limits are determined by enzyme structure and function.

• Psychrophile: Grows best at cold temperatures (0–15°C).

• Psychrotroph: Grows at refrigeration temperatures (0–30°C); responsible for food spoilage.

• Mesophile: Grows best at moderate temperatures (20–45°C); includes most human pathogens.

• Thermophile: Grows at high temperatures (45–70°C).

• Hyperthermophile: Grows at extremely high temperatures (>80°C).

pH and Microbial Growth

• Neutrophile: Grows best at neutral pH (~7); e.g., Escherichia coli.

• Acidophile: Grows best at low pH (<5.5); e.g., Lactobacillus.

• Alkalinophile: Grows best at high pH (>8); e.g., Bacillus alcalophilus.

Osmotic Pressure

• Obligate Halophile: Requires high salt concentrations for growth; e.g., Halobacterium.

• Facultative Halophile: Tolerates high salt but does not require it; e.g., Staphylococcus aureus.

Chemical Requirements for Growth

• Carbon: Backbone of all organic molecules; required for all cellular structures.

• Nitrogen: Needed for proteins, DNA, and RNA synthesis.

• Sulfur: Found in amino acids (cysteine, methionine) and some vitamins.

• Phosphorus: Component of ATP, nucleic acids, and cell membranes.

Oxygen Requirements and Toxicity

• Obligate Aerobes: Require oxygen; grow at the top of broth tubes.

• Obligate Anaerobes: Killed by oxygen; grow at the bottom.

• Facultative Anaerobes: Grow with or without oxygen; more growth at the top.

• Microaerophiles: Require low oxygen levels; grow just below the surface.

• Aerotolerant Anaerobes: Do not use oxygen but tolerate its presence; even growth throughout.

• Oxygen Toxicity: Oxygen can form reactive oxygen species (ROS) such as superoxide () and hydrogen peroxide (), which damage cellular components.

Biofilms

• Biofilm: A community of microorganisms attached to a surface and encased in a self-produced extracellular matrix.

• Medical Concern: Biofilms are highly resistant to antibiotics and immune responses, leading to persistent infections (e.g., on catheters, implants).

Culture Media Types

• Defined Media: Exact chemical composition is known.

• Complex Media: Contains extracts (e.g., peptone, beef extract); composition varies (e.g., nutrient broth).

• Selective Media: Inhibits growth of some organisms while allowing others (e.g., MacConkey agar selects for Gram-negative bacteria).

• Differential Media: Distinguishes organisms based on metabolic traits (e.g., lactose fermentation on MacConkey agar).

• Anaerobic Media: Supports growth of anaerobes (e.g., thioglycollate broth).

• Enrichment Media: Favors growth of a particular microbe (e.g., selenite broth for Salmonella).

Biosafety Levels (BSL)

CCC Lab Organisms: BSL-1

Quadrant Streak Plate Method

• Sterilize loop.

• Streak first quadrant.

• Flame loop, drag into second quadrant.

• Repeat for third and fourth quadrants.

• Purpose: To isolate single colonies from a mixed culture.

Bacterial Growth: Definitions and Phases

• Growth: Increase in the number of cells, not cell size.

• Generation Time: Time required for a cell to divide (or for a population to double).

• Determining Generation Time: Can be measured by plotting cell number over time and calculating the slope during exponential growth.

• Growth Phases:

  1. Lag phase: Adaptation, no division.

  2. Log (Exponential) phase: Rapid cell division.

  3. Stationary phase: Nutrient depletion, growth rate = death rate.

  4. Death phase: Cell death exceeds division.

• Semi-log Paper: Used because bacterial growth is exponential; log scale linearizes the data for easier analysis.

Measuring Microbial Growth

• Direct Methods: Count actual cells (living or total).

• Indirect Methods: Estimate cell numbers based on activity or mass.

Chapter 5: Microbial Metabolism

Basic Definitions

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules, releases energy.

• Anabolism: Synthesis of molecules, requires energy.

• Metabolic Pathway: Series of enzyme-catalyzed reactions converting a substrate to a final product.

ATP: The Energy Currency

• ATP (Adenosine Triphosphate): Stores energy in high-energy phosphate bonds.

• Uses: Biosynthesis, transport, movement.

Enzymes and Their Function

• Enzyme: Protein catalyst that speeds up reactions by lowering activation energy.

• Substrate: Molecule acted upon by the enzyme.

• Active Site: Region on enzyme where substrate binds.

• Activation Energy: Energy required to initiate a reaction.

• Induced Fit: Enzyme changes shape to fit substrate upon binding.

Factors Affecting Enzyme Activity

• Temperature, pH, substrate concentration, and inhibitors.

• Competitive Inhibition: Inhibitor competes with substrate for active site.

• Noncompetitive (Allosteric) Inhibition: Inhibitor binds elsewhere, changing enzyme shape and function.

Feedback Inhibition

• End product of a pathway inhibits an early enzyme, preventing overproduction and conserving resources.

Redox Reactions and Electron Carriers

• Redox Reaction: Involves transfer of electrons; oxidation is loss, reduction is gain.

• NAD+ and FAD: Electron carriers that shuttle electrons during metabolic reactions.

Stages of Aerobic Carbohydrate Catabolism

• Electron Transport Chain produces the most ATP.

Glycolysis: Two Major Stages

• Energy Investment Phase: Uses 2 ATP to phosphorylate glucose.

• Energy Payoff Phase: Produces 4 ATP (net gain 2), 2 NADH, and 2 pyruvate per glucose.

Alternative Pathways

• Entner-Doudoroff Pathway: Alternative to glycolysis; used by Pseudomonas and some other bacteria.

Krebs Cycle: Inputs and Outputs

• Input: Acetyl-CoA

• Outputs: CO2, NADH, FADH2, small amount of ATP

• Most energy is stored in NADH and FADH2 at the end of the cycle.

Electron Transport Chain and Chemiosmosis

• Electrons from NADH and FADH2 pass through a series of carriers, releasing energy.

• Energy is used to pump H+ ions across the membrane, creating a proton gradient.

• ATP Synthase uses this gradient to generate ATP (oxidative phosphorylation).

• Chemiosmosis: Movement of protons back across the membrane drives ATP synthesis.

Summary Equation for Aerobic Respiration

Aerobic vs. Anaerobic Respiration

• Aerobic Respiration: Oxygen is the final electron acceptor.

• Anaerobic Respiration: Other inorganic molecules (e.g., nitrate, sulfate) serve as final electron acceptors.

Fermentation

• Occurs when oxygen is absent; no electron transport chain.

• Uses organic molecules as final electron acceptors.

• Purpose: Regenerate NAD+ for glycolysis.

Common Fermentation Pathways

• Homolactic Fermentation: Produces only lactic acid (e.g., Lactobacillus).

• Heterolactic Fermentation: Produces lactic acid, CO2, and ethanol.

Catabolism of Fats and Proteins

• Fats: Broken down into glycerol and fatty acids; enter glycolysis and Krebs cycle.

• Proteins: Broken down into amino acids, deaminated, and enter metabolic pathways.

• Protein catabolism often indicates starvation, as cells use proteins when other sources are depleted.

Comparison Table: Respiration and Fermentation

Classification by Carbon and Energy Source