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 fundamental differences in cell structure and genetics.

• 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; include 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.

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, such as the human body.

• Transient Microbiota: Microbes that are temporarily found in a particular environment.

Naming Microorganisms

Microorganisms are named using the binomial system: Genus species (e.g., Escherichia coli). The genus is capitalized, the species is lowercase, and both are italicized. The name often provides information about the organism's characteristics or discoverer.

Key Historical Figures and Concepts

• Carl Woese: Developed the three-domain system based on ribosomal RNA sequencing.

• Spontaneous Generation: The disproven idea that life arises from nonliving matter.

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

• Louis Pasteur's Swan-Necked Flask Experiment: Demonstrated that microorganisms do not arise by spontaneous generation; air could enter the flask, but microbes were trapped in the neck.

• Germ Theory of Disease: States that specific diseases are caused by specific microorganisms.

• Antibiotics: Substances produced by microorganisms that inhibit or kill other microbes.

Taxonomy vs. Phylogenetics

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

• Phylogenetics: The study of evolutionary relationships among organisms.

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 bacteria.

Classification of Eukaryotes, Prokaryotes, and Viruses

• Eukaryotic Species: Defined by the ability to interbreed and produce fertile offspring.

• Prokaryotic Species: Defined by genetic similarity (often 97% or greater 16S rRNA sequence identity).

• Classification of Viruses: Based on nucleic acid type, replication strategy, and morphology.

Biochemical Tests

Used to identify microorganisms based on metabolic activities (e.g., fermentation, enzyme production).

Functional Anatomy of Prokaryotic and Eukaryotic Cells

Morphology and Bacterial Shapes

Bacteria exhibit various shapes, which can be important for identification.

• 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.

Structure and Function of Prokaryotic Cell Components

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

• Peptidoglycan: Main component of bacterial cell walls; crosslinking differs between Gram-positive and Gram-negative bacteria.

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

• Gram-Negative Bacteria: Thin peptidoglycan, 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: Lysozyme and antibiotics (e.g., penicillin) can disrupt cell wall synthesis.

Motility

• Flagella: Provide motility; advantageous for seeking nutrients or escaping harmful environments.

Passive and Active Transport Processes

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

• Active Transport: Requires energy (ATP) to move substances against their concentration gradient.

Nucleoid

Region in prokaryotic cells containing the single, circular DNA chromosome.

Ribosomes

Sites of protein synthesis; prokaryotic ribosomes are 70S, eukaryotic are 80S.

Inclusions

Reserve deposits found in prokaryotic cells (e.g., glycogen, polyphosphate granules).

Endospores

Dormant, highly resistant structures formed by some bacteria (e.g., Bacillus, Clostridium) for survival in harsh conditions.

Eukaryotic Flagella and Cilia

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

• Cilia: Short, numerous projections 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 cellular respiration.

• Chloroplasts: Site of photosynthesis in plants and algae.

Microscopy and Staining

Light vs. Electron Microscopy

• Light Microscopy: Uses visible light; suitable for observing live cells and stained specimens.

• Electron Microscopy: Uses electron beams; higher resolution; used for detailed ultrastructure.

Types of Light Microscopy

• Brightfield: Standard; requires staining.

• Darkfield: Enhances contrast in unstained samples.

• Phase-Contrast: Visualizes living cells without staining.

• Fluorescence: Uses fluorescent dyes; specific labeling.

Transmission Electron Microscopy (TEM) vs. Scanning Electron Microscopy (SEM)

• TEM: Provides detailed internal structures; thin sections.

• SEM: Provides 3D images of surfaces.

Gram Staining

1. Crystal violet (primary stain)

2. Iodine (mordant)

3. Alcohol (decolorizer)

4. Safranin (counterstain)

Result: Gram-positive bacteria appear purple; Gram-negative appear pink/red.

Acid-Fast Staining

1. Carbolfuchsin (primary stain)

2. Heat (to drive stain in)

3. Acid-alcohol (decolorizer)

4. Methylene blue (counterstain)

Result: Acid-fast bacteria (e.g., Mycobacterium) appear red; non-acid-fast appear blue.

Endospore Stain

1. Malachite green (primary stain, with heat)

2. Water (decolorizer)

3. Safranin (counterstain)

Result: Endospores appear green; vegetative cells appear red/pink.

Microbial Growth

Physical and Chemical Requirements for Growth

• Temperature: Microbes have optimal temperature ranges.

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

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

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

Temperature Classifications

• Psychrophiles: Grow at 0–15°C

• Psychrotrophs: Grow at 0–30°C (cause food spoilage)

• Mesophiles: Grow at 10–50°C (most human pathogens)

• Thermophiles: Grow at 40–70°C

• Hyperthermophiles: Grow at 65–110°C

Bacterial Oxygen Preferences

Biofilm Organization

• Biofilms: Communities of microorganisms attached to a surface and embedded in a self-produced matrix.

• Medical Significance: Biofilms are resistant to antibiotics and immune responses; important in device-related infections.

Types of Culture Media

• Defined Media: Exact chemical composition is known.

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

• Selective Media: Suppresses unwanted microbes, encourages desired microbes.

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