History of Microbiology and Classification of Microbes

Main Differences Between Bacteria, Archaea, and Eukarya

The three domains of life—Bacteria, Archaea, and Eukarya—are distinguished by differences in cell structure, genetics, and biochemistry.

• Bacteria: Prokaryotic cells lacking a nucleus; cell walls contain peptidoglycan; reproduce by binary fission.

• Archaea: Prokaryotic cells; cell walls lack peptidoglycan; often found in extreme environments; unique membrane lipids.

• Eukarya: Eukaryotic cells with a true nucleus and membrane-bound organelles; includes fungi, algae, protozoa, plants, and animals.

Fungi are eukaryotic, have chitin in their cell walls, and obtain nutrients by absorption. Algae are photosynthetic eukaryotes with cellulose cell walls. Protozoa are unicellular eukaryotes, often motile, and lack cell walls.

Viruses

Viruses are acellular infectious agents composed of nucleic acid (DNA or RNA) enclosed in a protein coat. They require a host cell to replicate.

Microbiota

• Stable (Resident) Microbiota: Microorganisms that are consistently present in a particular environment or host.

• Transient Microbiota: Microorganisms that temporarily colonize a host.

Naming Microorganisms

Microorganisms are named using the binomial nomenclature system: Genus species (e.g., Escherichia coli). The genus name is capitalized, the species name is lowercase, and both are italicized.

Carl Woese

Carl Woese proposed the three-domain system based on differences in ribosomal RNA (rRNA) sequences, leading to the classification of Bacteria, Archaea, and Eukarya.

Spontaneous Generation vs. Biogenesis

• Spontaneous Generation: The (disproven) idea that life can arise from nonliving matter.

• Biogenesis: The principle that living organisms arise only from preexisting living organisms.

Louis Pasteur and the Swan-Necked Flask Experiment

Pasteur's experiment used flasks with long, curved necks to show that microorganisms do not arise spontaneously but come from other microbes in the air, supporting biogenesis.

Germ Theory of Disease

The germ theory states that specific diseases are caused by specific microorganisms. This was a major shift from earlier beliefs about disease causation.

Antibiotics

Antibiotics are substances produced by microorganisms (or synthetically) that inhibit the growth of or destroy other microorganisms, especially bacteria.

Taxonomy vs. Phylogenetics

• Taxonomy: The science of classifying organisms based on shared characteristics.

• Phylogenetics: The study of evolutionary relationships among organisms, often using genetic data.

Theory of Endosymbiosis

This theory proposes that eukaryotic organelles such as mitochondria and chloroplasts originated from symbiotic prokaryotes.

• Supporting Evidence: Mitochondria and chloroplasts have their own DNA, double membranes, and ribosomes similar to those of bacteria.

Classification of Eukaryotes and Prokaryotes

• Eukaryotic Species: Defined as a group of closely related organisms that can interbreed.

• Prokaryotic Species: Defined as a population of cells with similar characteristics; often classified by genetic similarity.

Classification of Viruses

Viruses are classified based on their nucleic acid type (DNA or RNA), structure, replication method, and host range.

Biochemical Tests

Biochemical tests are used to identify microorganisms based on their metabolic activities (e.g., fermentation, enzyme production).

Functional Anatomy of Prokaryotic and Eukaryotic Cells

Morphology: Bacterial Shapes

• Coccus: Spherical

• Bacillus: Rod-shaped

• Spirillum: Spiral-shaped

• Vibrio: Comma-shaped

• Spirochete: Flexible spiral

Morphological Plasticity

Some bacteria can change shape in response to environmental conditions, a phenomenon known as morphological plasticity.

Structure and Function of Prokaryotic Cell Components

• Cell Wall: Provides shape and protection; medical significance includes antibiotic targeting.

• Plasma Membrane: Selective barrier for transport.

• Flagella: Motility structures; can contribute to pathogenicity.

• Pili/Fimbriae: Attachment and conjugation.

• Nucleoid: Region containing the bacterial chromosome.

• Ribosomes: Sites of protein synthesis (70S in prokaryotes).

• Inclusions: Storage granules for nutrients or other substances.

• Endospores: Highly resistant structures formed by some bacteria for survival under harsh conditions.

Advantage of Motility

Motility allows bacteria to move toward favorable environments (chemotaxis) or away from harmful substances.

Cell Wall of Bacteria

• Peptidoglycan: Main component; provides rigidity.

• Gram-Positive Bacteria: Thick peptidoglycan layer, teichoic acids.

• Gram-Negative Bacteria: Thin peptidoglycan layer, outer membrane with lipopolysaccharide (LPS).

• Mycoplasma: Lack cell walls; have sterols in the membrane.

• Mycobacteria: Waxy cell wall with mycolic acids; acid-fast.

• Damage to Cell Wall: Antibiotics like penicillin target peptidoglycan synthesis.

Passive and Active Processes

• Passive Transport: Movement of substances down their concentration gradient (e.g., diffusion, osmosis, facilitated diffusion).

• Active Transport: Movement against the gradient using energy (e.g., ATP-driven pumps).

Nucleoid

The nucleoid is the region in prokaryotic cells where the circular DNA chromosome is located.

Ribosomes

Prokaryotic ribosomes are 70S (composed of 50S and 30S subunits); eukaryotic ribosomes are 80S (60S and 40S subunits).

Inclusions

Inclusions are reserve deposits found in prokaryotic and eukaryotic cells, such as glycogen granules, polyphosphate granules, and gas vesicles.

Endospores

Endospores are dormant, tough, and non-reproductive structures produced by certain bacteria (e.g., Bacillus, Clostridium) to survive extreme conditions.

Eukaryotic Flagella and Cilia

• Flagella: Long, whip-like structures for movement.

• Cilia: Short, hair-like structures for movement or moving substances along surfaces.

Cell Walls of Eukaryotes

• Fungi: Chitin

• Algae: Cellulose

• Plants: Cellulose

• Animals: Lack cell walls

Mitochondria and Chloroplasts

• Mitochondria: Site of ATP production via aerobic respiration; contain their own DNA.

• Chloroplasts: Site of photosynthesis in plants and algae; contain their own DNA.

Microscopy and Staining

Light vs. Electron Microscopy

• Light Microscopy: Uses visible light; suitable for viewing live or stained cells; resolution ~0.2 μm.

• Electron Microscopy: Uses electron beams; higher resolution (~0.002 μm); used for detailed ultrastructure.

Types of Light Microscopy

• Brightfield: Standard; requires staining.

• Darkfield: Enhances contrast in unstained samples.

• Phase-Contrast: Visualizes live, unstained cells.

• Fluorescence: Uses fluorescent dyes or proteins.

TEM vs. SEM

• Transmission Electron Microscopy (TEM): Provides detailed internal structures; electrons pass through thin sections.

• Scanning Electron Microscopy (SEM): Provides 3D images of surfaces; electrons scan the specimen surface.

Gram Staining Steps and Results

1. Crystal violet (primary stain)

2. Iodine (mordant)

3. Alcohol (decolorizer)

4. Safranin (counterstain)

• Gram-positive: Purple (retain crystal violet)

• Gram-negative: Pink/red (safranin)

Acid-Fast Staining Steps and Results

1. Carbolfuchsin (primary stain)

2. Heat (to drive stain in)

3. Acid-alcohol (decolorizer)

4. Methylene blue (counterstain)

• Acid-fast bacteria: Red (retain carbolfuchsin)

• Non-acid-fast: Blue

Endospore Stain

Uses malachite green (stains endospores) and safranin (counterstains cells). Endospores appear green, vegetative cells red.

Microbial Growth

Physical and Chemical Requirements for Growth

• Temperature: Microbes have optimal, minimum, and maximum growth temperatures.

• pH: Most bacteria prefer neutral pH (6.5–7.5).

• Osmotic Pressure: High salt or sugar can inhibit growth.

• Chemical Requirements: Carbon, nitrogen, sulfur, phosphorus, trace elements, oxygen, and organic growth factors.

Temperature Classifications

Bacterial Oxygen Preferences

Biofilm Organization

Biofilms are structured communities of microorganisms attached to surfaces and embedded in a self-produced matrix. They are medically significant because they can resist antibiotics and immune responses.

Types of Culture Media

• Defined (Synthetic) Media: Exact chemical composition is known.

• Complex Media: Contains extracts and digests of yeasts, meat, or plants; composition varies.

• Selective Media: Inhibits unwanted microbes, encourages desired ones.

• Differential Media: Distinguishes between different types of microbes based on their biological characteristics.