Comprehensive Study Notes: Foundations of Microbiology

1. The Microbial World

Introduction to Microbes

Microbiology is the study of microscopic organisms, including bacteria, archaea, fungi, protozoa, and algae. These organisms play essential roles in ecosystems, human health, and industry.

• Definition: Microbes are unicellular or multicellular organisms invisible to the naked eye.

• Interactions: Digestion, disease, food production, biotechnology.

• Characteristics of Life: Cell structure, metabolism, growth/reproduction, genetic variation, adaptation, homeostasis.

Macromolecules

• Proteins: Enzymes, structural components.

• Lipids: Membranes, energy storage.

• Carbohydrates: Energy, structure.

• Nucleic Acids: DNA and RNA, genetic information.

Domains of Life

• Bacteria

• Archaea

• Eukarya

Viruses

• Definition: Acellular, not classified as living, replicate only in hosts.

• Applications: Disease, genetic tools, industrial uses.

Key Discoveries

• Leuwenhoek: First observations of microbes (microscopes).

• Pasteur: Disproved spontaneous generation.

• Koch: Developed postulates for disease causation (anthrax).

Historical Impact

• Black Death: Major pandemic; advances in prevention and treatment reduced mortality in the 20th century.

2. Bacteria

General Features

Bacteria are prokaryotic microorganisms with diverse shapes, structures, and metabolic capabilities.

• Morphology: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral), vibrios (comma-shaped), pleiomorphic forms. Some form hyphae or mycelia.

• Cytoplasm: Contains nucleoid (DNA), ribosomes, plasmids.

• Cytoskeleton: FtsZ (cell division), MreB (cell shape), ParM (plasmid segregation).

• Cell Envelope: Phospholipid membrane, selective permeability, energy capture (proton motive force).

• Cell Wall: Peptidoglycan; Gram+ (thick wall), Gram– (thin wall + outer membrane with lipopolysaccharide).

Surface Structures

• Flagella: Motility.

• Pili: Adhesion, conjugation.

• Capsules: Protection, evasion.

• S-layers: Protein arrays.

Diversity and Classification

• Classification: Based on morphology, growth, physiology, DNA sequence.

• Distinct Domain: Carl Woese (1970s) established Bacteria as a separate domain using rRNA sequencing.

Cell Structure

• Size: 0.5–5 μm.

• No histones: Unlike eukaryotes.

• Unique plasma membranes: Isoprenoids, ether linkages, monolayers possible (especially in Archaea).

• Cell wall: Pseudomurein (in Archaea) instead of peptidoglycan.

• Surface: S-layers, capsules, unique flagella.

Diversity in Archaea

• Euryarchaeota: Methanogens, halophiles, thermophiles.

• TACK: Thaumarchaeota (important in nitrogen cycling), Korarchaeota.

• DPANN: Nanoarchaeota (symbionts).

• Asgard: Possible link to eukaryotic evolution.

3. Eukaryal Microorganisms

General Features

Eukaryal microorganisms include fungi, protozoa, and algae. They possess membrane-bound organelles and a cytoskeleton.

• Features: Nucleus, organelles, phospholipid bilayer, cytoskeleton.

• Organelles: Mitochondria (ATP production), chloroplasts (photosynthesis), ER, Golgi, ribosomes.

• Cell Walls: Cellulose (plants), chitin (fungi).

Diversity and Examples

• Saccharomyces cerevisiae: Yeast, model for genetics.

• Giardia duodenalis: Protozoan, causes disease via mitochondrial loss.

• Chlamydomonas: Algae, model for cell signaling and motility.

• Diatoms: Silica cell walls, photosynthetic.

Replication and Origin

• Replication: Mitosis, meiosis; alternation between haploid/diploid.

• Origin: Endosymbiotic theory (mitochondria, chloroplasts from bacteria).

• Diversity: Includes pathogens, sleeping sickness, fungal infections, producers, degraders, photosynthesizers.

5. Viruses

General Features

Viruses are acellular infectious agents that require host cells for replication. They are significant in disease, biotechnology, and genetic research.

• Definition: Infectious agents, replicate only in hosts.

• History: Ivanovski (TMV), Beijerinck (virus concept), Reed (yellow fever), Twort & d'Herelle (bacteriophages).

• Structure:

  • Size: 10–100 nm

  • Genome: DNA or RNA, single-stranded (ss) or double-stranded (ds), linear or circular, single or segmented.

Classification

• Capsid: Protein shell, helical, icosahedral, complex shapes.

• Envelope: Lipid-derived membrane; viruses may be naked or enveloped.

• Origins: Coevolution, regressive, progressive/hybrids.

Cultivation and Quantification

• Cultivation: Plaques (phages), cytopathic effects (animal viruses).

• Quantification: Direct counts, hemagglutination, plaque assays, endpoint assays.

Virus-like Particles

• Viroids: Infectious RNA.

• Satellites: Require helper viruses.

• Virophages: Infect other viruses.

• Prions: Infectious proteins.

9. Viral Replication Strategies

Overview

Viruses employ diverse strategies to infect host cells and replicate their genomes, depending on their structure and genome type.

• Recognition: Host range determined by viral attachment proteins (e.g., influenza HA).

• Entry/Uncoating:

  • Enveloped viruses: Endocytosis (pH-dependent), membrane fusion (HIV).

  • Bacteriophages: Inject genomes.

  • Plant viruses: Entry via physical damage.

• Replication:

  • DNA viruses: Use host enzymes (e.g., poxviruses).

  • RNA viruses: RNA-dependent RNA polymerase.

  • Retroviruses: Reverse transcriptase, integrase, provirus formation.

• Assembly:

  • Capsid self-assembly.

  • Enveloped viruses bud; naked/phages lyse.

7. Cultivating Microorganisms

Factors Affecting Growth

Microbial growth is influenced by nutrient availability, environmental conditions, and laboratory techniques.

• Nutrients: Phototrophs, chemotrophs, autotrophs, heterotrophs, auxotrophs.

• Oxygen: Aerobes, anaerobes, facultatives.

• Other factors: Pressure, temperature.

Laboratory Growth

• Media: Liquid, solid, complex, defined, selective, differential, enriched.

• Pure cultures: Streak, spread, pour plates.

• Unculturable bacteria: RNA sequencing, metagenomics.

Measuring Growth

• Direct counts: Chambers.

• Viable counts: Colony-forming units (CFU).

• Turbidity: Spectrophotometry.

23. Eukaryal Pathogenesis

Mechanisms and Examples

Eukaryal pathogens employ various strategies to infect hosts, evade defenses, and acquire nutrients. Understanding these mechanisms is crucial for disease prevention and treatment.

• Mechanisms: Gain access, evade defenses, acquire nutrients.

• Examples:

  • Toxoplasma gondii: Evasion via protein interactions.

  • Plasmodium falciparum: Vector transmission (malaria).

  • Trypanosoma brucei: Immune evasion.

  • Candida albicans: Opportunistic infection, nutrient acquisition.

  • Magnaporthe oryzae: Plant pathogen.

• Plasmodium falciparum:

  • Causes malaria; attaches to RBCs via MSP proteins.

  • Treated/prevented by blocking interactions and antimalarials.

• Macroscopic Pathogens:

  • Helminths (Ascaris lumbricoides, Schistosoma mansoni).

  • Microscopic eggs and larvae play key roles in transmission.

Surface Structures and Pathogenesis Table

The following table summarizes key surface structures and their roles in pathogenesis:

Structure	Function	Example Organism
Flagella	Motility	Escherichia coli
Pili	Adhesion, conjugation	Neisseria gonorrhoeae
Capsule	Immune evasion	Streptococcus pneumoniae
S-layer	Protection, structure	Bacillus anthracis

Key Equations in Microbial Growth

• Exponential Growth:

$N_t = N_0 e^{ ext{rt}}$

• Generation Time:

$g = \frac{t}{n}$

• Colony-Forming Units (CFU):

$\text{CFU/mL} = \frac{\text{Number of colonies}}{\text{Dilution factor} \times \text{Volume plated}}$

Additional info: Some details on Archaea and Eukaryal diversity were inferred from standard microbiology knowledge to provide context for fragmented notes.