Microbial Classification

The Three Domains

Microorganisms are classified into three major domains based on genetic and structural differences, particularly in ribosomal RNA (rRNA) sequences.

• Bacteria: Prokaryotic organisms lacking a nucleus.

• Archaea: Prokaryotes distinct from bacteria, often found in extreme environments.

• Eukarya: Includes fungi, plantae, animalia, and protista. All eukaryotes evolved from cells that formed over three billion years ago.

Conserved DNA: The DNA passed from ancestors is described as conserved, meaning it remains relatively unchanged over generations.

The Six Kingdoms

Organisms are further classified into six kingdoms:

• Bacteria

• Archaea

• Protista

• Plantae

• Fungi

• Animalia

Majority are Insects (Additional info: Insects are the most numerous group within Animalia.)

The Traditional Five Kingdoms

• Monera (Bacteria and Archaea)

• Protista

• Plantae

• Fungi

• Animalia

Endosymbiotic Theory

This theory explains the origin of eukaryotic organelles, suggesting that eukaryotes originated from infoldings of prokaryotic plasma membranes and that mitochondria and chloroplasts developed from endosymbiotic bacteria.

• Endosymbiont: Bacteria engulfed into organelles.

Some Algae Has Peptidoglycan

Cyanophora paradoxa is a model freshwater algae organism with a peptidoglycan layer.

• Cyanelles: PG layer

• Algal cell wall

Characteristics of Archaea, Bacteria, and Eukarya

These domains differ in cell structure, membrane composition, and genetic material.

Prokaryotic Cells and Eukaryotic Organelles Compared

Scientific Nomenclature

Binomial Naming System

Organisms are named using a two-part scientific name: genus and species. The genus is capitalized, and the species is lowercase, both italicized.

• European Robin: Erithacus rubecula

• American Robin: Turdus migratorius

• Dog: Canis familiaris (Note: The space is underlined in the original, indicating a formatting issue.)

Phylogenetic Relationships of Prokaryotes

Bacteria and Archaea

Bacteria and archaea are both prokaryotes but differ in genetic, biochemical, and structural features. Archaea often inhabit extreme environments.

Classification of Viruses

Virus Properties

Viruses are not classified as living organisms. They require host cells to replicate and can cause diseases such as measles, which is highly contagious.

• Measles: Outbreaks are common; 90% contagiousness.

• Suppression of immune system after recovery.

• Genetics determines how you react to viruses.

Classifying and Identifying Microorganisms

Identification Methods

• Bergey's Manual of Determinative Bacteriology: Lists identification schemes for bacteria and archaea.

• NIH Microbiology: Uses biochemical tests, serology, and PCR for classification.

Gram Staining: Differentiates bacteria into Gram-positive (thick peptidoglycan, teichoic acid) and Gram-negative (thin peptidoglycan, lipoteichoic acid).

• Gram +: Thick peptidoglycan, Gram + TA (teichoic acid) and LTA (lipoteichoic acid)

• Bacteria in legs, orange thread

Fermentation Tests

• E. coli likes lactose → milk sugar

• Yellow and gas bubble indicate fermentation

Serology

• Rapid identification: Biochemical tests performed simultaneously

• Percentages indicate how much of the strain is identified

COVID-19 Testing

Types of Tests

• Molecular (RT-PCR): More accurate, looks at specific gene sequence

• Serology (Antibody Test): Quick test, detects antibodies

RT-PCR: Reverse transcriptase polymerase chain reaction, used for COVID-19 and HIV detection.

• COVID-19: Big test

• Looking at antibodies, bind, sample does poor → negative

• PCR: Polymerase chain reaction

DNA Fingerprints

• Banding pattern is unique for each organism

Nucleic Acid Amplification Tests (NAATs)

• Use of PCR to amplify DNA of unknown microorganisms that cannot be cultured

• Metagenomics: Study of genetic material from multiple organisms in a sample

Control of Microbial Growth

Physical Methods

• Freeze, fridge, oven, drier

• Physical, chemical, mechanical methods

• Don't preserve, microbes will eat it

• Physical: Jam, brine, salt, sugar, loss water, high osmotic

• Chemical: Food, add, dry out

Microbial Control Terminology

• Sepsis: Infection, bacterial contamination

• Asepsis: Prevention technique

• Antisepsis: Destroying harmful pathogens from living tissue

• Sterilization: Removal/destruction of all microorganisms, including endospores

• Sanitization: Lowering microbial levels to safe levels

• Disinfection: Destroying harmful microbes from surfaces

• Degerming: Mechanically removing microbes

• Bacteriostasis: Inhibiting growth of bacteria

Microbial Death Curve

It will take longer to kill all members of a larger population than a smaller one.

• Physical agents: Heat and radiation

• Chemical agents

• Mechanical removal methods: Filtration

Heat Sterilization

• Moist heat: Boiling, autoclave (121°C), kills endospores

• Dry heat: Flame, oven, incineration

• Oxidation

Cold Methods

• Refrigerator, freezer, lyophilization

• Suppresses growth, stasis

• Listeria grows in refrigerator

Radiation

• Ionizing radiation: X-ray, gamma ray

• Nonionizing radiation: UV, sunlight

• UV damages DNA, causes skin cancer

Mechanical Removal Methods

• Filtration: Liquid sterilized

• Air: HEPA filter

Chemical Agents

• Liquid and gas sterilization

• Formaldehyde: Cleans surface, not air

• Gaseous sterilants: Alkylation, cross-links nucleic acids and proteins

• Ethylene oxide: Used for heat-sensitive material, can destroy DNA

Antibiotics

• Kill or inhibit specific bacteria

• Mechanisms: Inhibit cell wall synthesis, protein synthesis, DNA replication

• Antibiotics only work on bacterial infection

Disk-Diffusion Method

• Tests susceptibility of bacteria to antibiotics

• Kirby-Bauer disk diffusion: Measures zone of inhibition

• Starch in agar absorbs toxins, so nutrient agar is used for results

Summary Table: Microbial Control Methods

Key Terms and Definitions

• Prokaryote: Organism without a nucleus (Bacteria, Archaea)

• Eukaryote: Organism with a nucleus (Fungi, Plantae, Animalia, Protista)

• Endosymbiosis: Theory that eukaryotic organelles originated from prokaryotes

• Gram Stain: Laboratory technique to differentiate bacteria

• Antibiotic: Chemical that kills or inhibits bacteria

• Sterilization: Complete destruction of all microbial life

• Disinfection: Removal of harmful microbes from surfaces

• Asepsis: Absence of pathogenic microbes

Important Equations

• Microbial Death Rate:

Where: = number of surviving organisms at time t = initial number of organisms = death rate constant = time

Examples and Applications

• Example: E. coli fermentation test: Yellow color and gas bubble indicate lactose fermentation.

• Application: PCR is used to detect COVID-19 by amplifying viral RNA.

• Example: UV radiation is used to sterilize surfaces in hospitals.

Additional info: Some context and explanations have been expanded for clarity and completeness, including definitions and examples relevant to Anatomy & Physiology students.