Microbiology Fundamentals: Bacteria, Archaea, and Laboratory Techniques

Microbiology

Study of living things too small to be seen without magnification.

Microbes

Include bacteria, archaea, protozoa, fungi, helminths, unicellular algae, viruses, and prions.

Bacteria and Archaea

Are prokaryotic, differing from eukaryotes in DNA packaging, cell wall composition (peptidoglycan in bacteria), and lack of membrane-bound organelles.

Bacterial structures

Include essential components like the cytoplasmic membrane, cytoplasm, ribosomes, cytoskeleton, and chromosome, with many also possessing a cell wall and glycocalyx.

External structures

Like flagella, fimbriae, pili, and nanowires facilitate motility, attachment, and communication.

Cell envelope

(Cell wall, cytoplasmic membrane, and outer membrane in Gram-negatives) is crucial for structural integrity and protection.

Endospores

Are highly resistant dormant structures formed by certain bacteria, medically significant for their survival in harsh conditions.

Archaea

Are a distinct domain, often extremophiles, sharing characteristics with both bacteria and eukaryotes but possessing unique features.

Five I's of Microbiology

(Inoculation, Incubation, Isolation, Inspection, Identification) are fundamental laboratory practices.

Microbial media

Vary by physical state, chemical composition (defined vs. complex), and functional type (general-purpose, enriched, selective, differential, reducing, transport, assay, enumeration).

Microscopy

Is essential for visualizing microbes, with different types (bright-field, dark-field, phase-contrast, fluorescence, confocal, TEM, SEM) offering varied capabilities in magnification, resolution, and contrast.

Staining techniques

(Simple, differential like Gram and Acid-Fast, and special like capsule and flagellar) are vital for visualizing and differentiating microbial cells.

Microbes are ubiquitous

Play critical roles in global biogeochemical cycles, photosynthesis, and human health (both beneficial and pathogenic).

Historical figures

Like Pasteur, Koch, Hooke, and Leeuwenhoek laid the groundwork for modern microbiology.

Macromolecules

(Carbohydrates, lipids, proteins, nucleic acids) are the building blocks of life, each with specific structures and functions.

Taxonomy

Provides a system for naming, classifying, and identifying microorganisms, with the Woese-Fox system recognizing three domains: Bacteria, Archaea, and Eukarya.

Evolutionary History

Single-celled organisms appeared ~3.8 billion years ago.

Eukaryotes

"True nucleus."

Prokaryotes

Bacteria and Archaea ("pre-nucleus").

Ubiquity

Found deep in Earth's crust, polar ice caps, oceans, inside plants/animals, and landscapes; essential to life.

Theory of Evolution

Accumulation of changes in organisms adapting to environments; well-tested scientific theory.

Photosynthesis

Anoxygenic - Did not produce oxygen (early bacteria); Oxygenic - Produces oxygen (evolved from anoxygenic); photosynthetic microorganisms responsible for 70% of Earth's photosynthesis.

Global Impact

Drive soil, water, and atmosphere composition; produce CO2, NO, CH4; bacteria/viruses abundant in oceans; associate with plants for nutrient uptake and disease protection.

Historical Uses

Bread, alcohol, cheese production; wound treatment; mining; bioremediation.

Genetic Engineering

Manipulating genetics for new products/GMOs.

Recombinant DNA Technology

Transferring genetic material, altering DNA.

Bioremediation

Using microbes to clean up pollutants.

Pathogens

Microbes causing disease (over 2,000 types).

Infectious Diseases

Major cause of death worldwide.

Emerging/Reemerging Diseases

AIDS, Hepatitis C, Zika, West Nile, Tuberculosis.

Noninfectious Disease Links

Gastric ulcers (Helicobacter pylori), multiple sclerosis, OCD, coronary artery disease, obesity linked to chronic infections.

Trends

Increasing infections in immunocompromised individuals; rise of drug-resistant microbes.

Viruses

Not independently living cells; hereditary material (DNA/RNA) in a protein coat, sometimes membrane.

Prions

Simpler than viruses; only protein, no nucleic acid; act as infectious microorganisms.

Spontaneous Generation

Belief that invisible vital forces created life.

Abiogenesis

Embraced spontaneous generation.

Biogenesis

Living things arise only from their own kind.

Louis Pasteur

Disproved spontaneous generation with swan-necked flask experiments; studied fermentation; invented pasteurization; linked human disease to infection.

Robert Hooke

Described cellular structures ('little structures').

Antonie van Leeuwenhoek

Manufactured simple microscopes; observed 'animalcules' in water and from teeth.

Ferdinand Cohn

Discovered heat-resistant endospores.

Oliver Wendell Holmes & Ignaz Semmelweis

Emphasized hand washing in hospitals.

Joseph Lister

Used aseptic techniques in surgery ('Father of antiseptic surgery').

Robert Koch

Developed Koch's postulates to link specific microbes to diseases (e.g., anthrax by Bacillus anthracis).

1970s

Discovery of restriction enzymes (molecular 'scissors') by Nathans, Arber, Smith; enabled genetic engineering.

1980s

Invention of PCR technique (polymerase chain reaction); amplifies tiny amounts of DNA for study, diagnosis, forensics.

2000s

Importance of small RNAs in regulating cell processes; new targets for antimicrobial therapy.

2010s and Beyond

Genetic identification of the Human Microbiome (HMP); revealed diverse but functionally similar microbial communities in humans.

Monomers

Subunits of macromolecules.

Polymers

Chains of monomers.

Carbohydrates

(CH2O)n; end in -ose.

Monosaccharides

Glucose, fructose, xylose.

Disaccharides

Lactose, maltose, sucrose.

Polysaccharides

Structural support, protection, nutrient/energy stores.

Triglycerides

Storage lipid (glycerol + 3 fatty acids); saturated/unsaturated; concentrated energy storage.

Phospholipids

Membrane lipids (hydrophilic head, hydrophobic tail); form bilayers, main component of cell membranes.

Steroids

Ringed compounds (cholesterol); reinforce cell membranes in eukaryotes and some bacteria.

Waxes

Ester of long-chain alcohol and fatty acid; waterproofing; found in cell walls of Mycobacterium (tuberculosis, leprosy).

Proteins

Predominant organic molecules; composed of 20 amino acids.

Peptide

Short chain of amino acids.

Polypeptide

>20 amino acids, often protein subunit.

Protein

Minimum 50 amino acids.

Primary (1°)

Amino acid sequence.

Secondary (2°)

Alpha helix, beta pleated sheet (hydrogen bonds).

Tertiary (3°)

Additional bonds, disulfide bonds.

Quaternary (4°)

Multiple polypeptides forming a protein.

Function

Unique 3D shape for specific interactions (lock and key); enzymes (catalysts), antibodies (immune defense).

Native State

Functional 3D form.

Denatured

Disruption of native state by heat, acid, alcohol, disinfectants.

DNA

Coded genetic program for heredity.

RNA

"Helper" molecules, carry out DNA instructions, translate into proteins.

DNA Structure

Double helix; two nucleotide strands linked by hydrogen bonds between nitrogen bases (Adenine-Thymine, Guanine-Cytosine).

RNA Types

mRNA (protein info), tRNA (amino acid carrier), rRNA (ribosome component), small RNAs (gene regulation).

ATP (Adenosine Triphosphate)

Energy molecule of cells; adenine, ribose, three high-energy phosphate molecules; releases energy when phosphate bond is broken.

Common Traits

Spherical, polygonal, cuboidal, or cylindrical; contain protoplasm encased in a cell membrane; have chromosomes (DNA); ribosomes for protein synthesis; complex function.

Eukaryotic Cells

Animals, plants, fungi, protozoa/unicellular algae; contain membrane-bound organelles.

Nomenclature

Assigning scientific names.

Binomial System

Genus + species (e.g., Escherichia coli or E. coli). Italicized in print, underlined handwritten.

Classification

Orderly arrangement into a hierarchy.

Ranks

Domain, Kingdom, Phylum/Division, Class, Order, Family, Genus, Species.

Identification

Discovering and recording traits for recognition and classification.

Phylogeny

Taxonomic scheme representing natural relatedness.

Evolution

Hereditary information changes over time, leading to structural/functional changes; natural selection favors survival.

Darwin/Haeckel

Plants, Animals, Protista, Monera.

R.H. Whittaker

Added Fungi (5 Kingdoms).

Woese-Fox System

Based on conserved small subunit ribosomal RNA (ssu 16S rRNA) sequences.

Three Domains

Bacteria, Archaea, Eukarya.

Inoculation

Introducing a small sample (inoculum) into a nutrient medium to culture microbes.

Incubation

Placing inoculated media in a temperature-controlled chamber (incubator) (20-45°C) to encourage microbial multiplication.

Isolation

Separating individual microbial cells to grow discrete mounds of cells (colonies) on a solid medium.

Colony

Macroscopic cluster from a single cell (or Colony Forming Unit - CFU).

Inspection

Observing cultures macroscopically and microscopically.

Identification (Microbiology)

Determining the type of microbe through microscopic appearance, cellular metabolism, nutrient requirements, enzyme production, genetic, and immunologic characteristics.

Types of Media

Different types of media used in microbiology for culturing microbes.

Liquid Media

Broths.

Semisolid Media

Contains agar (0.3-0.5%), used for motility tests.

Solid (liquefiable) Media

Contains agar (1-5%), solid at room temp, liquefies at 100°C, solidifies at 42°C. Not digestible by most microbes.

Solid (non-liquefiable) Media

Cooked meat media, potato slices.

Defined (Synthetic) Media

Precisely chemically defined composition; exact formula.

Complex Media

One or more components not chemically defined (e.g., extracts of animals, plants, yeasts; blood, serum, peptone).