Microbiology: Key Concepts, Microorganisms, and Techniques

Microbiology

Branch of biology that studies living things too small to be seen without magnification.

Major groups of microorganisms

Bacteria, Archaea, Protists, Fungi, and Viruses.

Bacteria

Single-celled prokaryotes found everywhere; vital for nutrient cycling, decomposition, and sometimes disease.

Archaea

Prokaryotes that often live in extreme environments; genetically distinct from bacteria.

Protists

Single-celled eukaryotes including algae (photosynthetic) and protozoa (heterotrophic).

Fungi

Mostly multicellular eukaryotes like molds and yeasts that decompose organic matter.

Viruses

Acellular entities composed of nucleic acid and protein that rely on host cells for replication.

Importance of microorganisms

Essential for ecosystems, biotechnology, and human health.

Microorganisms in ecology

Drive photosynthesis, decomposition, and nutrient cycling.

Microorganisms in biotechnology

Used for biofuel production, wastewater treatment, and bioremediation.

Microorganisms in human health

Can be pathogenic or beneficial; aid digestion, immunity, and vitamin synthesis.

Wolbachia example

Bacteria that reduce spread of dengue virus in mosquitoes.

Antonie van Leeuwenhoek

Invented the first microscope in 1677; first to observe microorganisms.

Louis Pasteur

Disproved abiogenesis, developed pasteurization, and contributed to germ theory of disease.

Robert Koch

Proved bacteria cause disease and developed methods for growing bacteria on solid media.

Edward Jenner

Developed first vaccination for smallpox in 1796.

Joseph Lister

Pioneer of aseptic technique in the early 1900s.

Carl Woese

Used rRNA as a taxonomic marker; developed the three-domain system.

Norman Pace

Used 16S rRNA sequencing to identify and classify microbes.

Prokaryotic cell

Cell without a membrane-bound nucleus or organelles; includes bacteria and archaea.

Eukaryotic cell

Cell with a true nucleus and membrane-bound organelles; includes protists, fungi, plants, and animals.

Viruses classification

Neither prokaryotic nor eukaryotic; nonliving infectious particles.

Woese-Fox three domain system

Bacteria, Archaea, Eukarya.

Whittaker five kingdom system

Monera, Protista, Fungi, Plantae, Animalia.

Binomial nomenclature

System of naming organisms using Genus and species.

Pathogen

Microbe that causes disease.

Germ theory of disease

Diseases are caused by microorganisms, not spontaneous generation.

Aseptic technique

Methods used to prevent contamination by unwanted microorganisms.

Taxonomy

Science of classifying, naming, and identifying organisms.

Onesimus

African man who introduced smallpox inoculation to colonial Boston.

Angelina Hesse

Introduced agar as a culture medium, revolutionizing microbiology.

Esther Lederberg

Discovered lambda phage; contributed to understanding of gene regulation and horizontal gene transfer.

Importance of diversity in science

Inclusion broadens perspectives and innovation, benefiting all communities.

Six I's of microbiology

Inoculation, Incubation, Isolation, Inspection, Information gathering, Identification.

Inoculation

Introducing a sample into medium that supports microbial growth using sterile tools.

Incubation

Maintaining cultures in controlled conditions (temperature, oxygen, light, moisture).

Isolation

Separating individual species to form pure cultures.

Inspection

Examining cultures for cell morphology, arrangement, or staining.

Information gathering

Conducting biochemical, genetic, or molecular tests to characterize organisms.

Identification

Determining an organism's species or strain using metabolic or genetic traits.

Why microorganisms are difficult to study

They exist in complex communities, require artificial growth conditions, and are microscopic.

Physical states of media

Liquid (broth), Solid (agar), and Semi-solid.

Liquid media

Used for fast, large-volume growth.

Solid media

Used for isolation and long-term storage; can be liquefiable or not.

Semi-solid media

Used to test motility and oxygen preferences (0.3-0.5% agar).

Synthetic media

Precisely defined chemical composition.

Complex media

Contains ingredients like yeast or beef extract; not chemically defined.

General-purpose media

Supports wide range of microbes (e.g., TSA).

Enriched media

Contains nutrients for fastidious organisms (e.g., blood agar).

Selective media

Promotes growth of certain microbes while inhibiting others.

Differential media

Distinguishes different microbes based on appearance or metabolic reaction (e.g., MSA).

Inoculation techniques

Streak plate, pour plate, spread plate.

Streak plate

Cells spread over agar to isolate colonies.

Pour plate

Sample diluted and mixed with molten agar.

Spread plate

Known volume spread evenly over agar.

Aseptic technique importance

Prevents contamination during culture handling.

Optical microscope

Uses visible light and glass lenses for magnification.

Magnification

Ability to make image appear larger; total magnification = objective × ocular lens.

Resolution

Ability to distinguish two points as separate; depends on wavelength and numerical aperture.

Oil immersion

Improves resolution by reducing light scattering.

Bright-field microscope

Specimen appears dark against bright background; most common.

Dark-field microscope

Shows bright specimen on dark background; useful for motile, unstained microbes.

Phase-contrast microscope

Enhances internal detail in live cells.

Fluorescence microscope

Uses UV light and fluorescent dyes to tag molecules.

Confocal microscope

Fluorescence technique producing 3D images by scanning optical sections.

Transmission electron microscope (TEM)

Shows internal structure by passing electrons through thin sections.

Scanning electron microscope (SEM)

Scans specimen surface for 3D external details.

Live preparation

Allows observation of living, moving cells (e.g., wet mount).

Fixed preparation

Cells are killed, fixed, and stained for long-term viewing.

Simple stain

Uses single dye to show shape and size.

Differential stain

Differentiates types of cells or structures (e.g., Gram, acid-fast, endospore).

Gram stain

Differentiates Gram-positive (purple) and Gram-negative (pink/red) bacteria.

Acid-fast stain

Identifies Mycobacterium species.

Endospore stain

Highlights spore-forming bacteria.

Structural stains

Reveal specific parts like capsules or flagella.

Positive stain

Dye binds to cells.

Negative stain

Dye stains background, leaving cells clear.

Prokaryote characteristics

Unicellular, lack nucleus and organelles; domains Bacteria and Archaea.

Prokaryotic external components

S-layer, glycocalyx, flagella, pili, fimbriae.

Prokaryotic cell envelope

Cell wall, outer membrane, plasma membrane.

Prokaryotic internal components

Cytoplasm, ribosomes, nucleoid, plasmids, inclusions, endospores.

S-layer

Protein lattice providing protection and structure; helps attachment and survival.

Glycocalyx

Polysaccharide coating (capsule or slime layer) protecting from desiccation, toxins, and phagocytosis.

Biofilm

Community of microbes adhering to surfaces for protection and cooperation.

Flagella

Provide motility through runs and tumbles; respond to chemical signals (chemotaxis).

Fimbriae

Short, hairlike structures used for attachment.

Pili

Tubular structures used for DNA exchange (conjugation).

Cell wall

Peptidoglycan layer providing shape and protection from osmotic pressure.

Outer membrane

Found in Gram-negative bacteria; contains LPS and porins.

Lipopolysaccharides (LPS)

Outer membrane components that act as permeability barrier and contribute to pathogenicity.

Plasma membrane

Phospholipid bilayer with proteins; site of metabolism and selective transport.

Cytoplasm

Water-rich interior for metabolism and biosynthesis.

Nucleoid

Region containing circular bacterial DNA.

Plasmid

Small circular DNA carrying resistance or virulence genes; transferable between cells.

Ribosome

Protein synthesis site (70S in prokaryotes).

Inclusion bodies

Storage of nutrients or materials like magnetite.

Endospore

Dormant, resistant cell for survival in harsh environments; formed by Bacillus and Clostridium.

Gram-positive cell wall

Thick peptidoglycan, teichoic acids present, no outer membrane.

Gram-negative cell wall

Thin peptidoglycan, no teichoic acids, outer membrane with LPS and porins.

Periplasmic space

Small in Gram-positive, large in Gram-negative.