BIOL 260-General Microbiology
Instructor: Christopher Thor
Masters Degree, Bioengineering
Bachelors Degree, Molecular Biology

Welcome to BIOL 260: Microbiology!
• First day:
– Review of Syllabus
– Sign-in
– Introduce the course, review course expectations
– Begin with first lab
• Exercise 3: Microscope Lab

Objectives for today
• Define prokaryotes, eukaryotes & their classification
• Give a historical perspective on medical bacteriology
• Introduction to bacterial stains and images

What is microbiology?
• The scientific discipline which studies microbes or microorganisms
– Biology of microbes
– The interaction of microbes with other microbes, the environment, and humans

The “Yotes”
Definitions:
Prokaryote: Single celled organism, no nucleus.
Bacteria, Archaea
Eukaryote: Single or multi-celled organism, membrane bound nucleus
Algae, Protozoa, Fungi, people

What are examples of microbes?
• Algae
• Fungi
• Protozoa
• Bacteria
• Viruses
Which are Prokaryotes are which are Eukaryotes?

Hierarchy

Types of Microbes: Algae

Types of Microbes: Protozoa

Types of Microbes: Fungi

Types of Microbes: Bacteria

Viruses, Viroids, Prions

Microorganisms are associated with
• Disease
– Cause of many epidemics in history
– Bubonic plague (1346-1350)
• Killed 25 million people
– Small pox
• Killed estimated 600 million people since 10,000 BC
• Eradicated in 1979
– HIV
• 3.1 million estimated new cases per year
• 5% of Sub-Saharan Population
– Malaria
Small Pox

Bacteria are associated with
• Normal microbiota (normal flora)
– The bacteria that are present on our bodies

Bacteria are associated with
• The environment
– Rhizobium
(the greatest bacteria you’ve never heard of)
• Nitrogen fixation in the soil
• Food products
– Beer! Or bread, wine, sauerkraut, yogurt, cheese…
• Medicines
– Bacteria are “programmed” to make insulin

History of Microbiology
• It all started with the microscope!
– Zacharis Janssen (1600)
– Antoni van Leewenhoek (1632-1723)
– Robert Hooke (1665)

Zacharis Janssen ’ s microscope
• Modeled after the telescope
• Consisted of two lenses
• Magnified images 3-
10X

Leewenhoek ’ s microscope
20-30x magnification

Where do cells come from?
• Spontaneous generation
– Francesco Redi (1668)
• Spontaneous Generation does not occur
– John Needham (1745)
• Spontaneous Generation does occur
– Lazzaro Spallanzani (1765)
– Louis Pasteur (1861)
• Biogenesis
– Rudolf Virchow (1858)
• Living things come from living things

Pasteur ’ s flasks

John Tyndall questions Pasteur ’ s experiments
• Could not reproduce Pasteur ’ s results
– Specific growth media required
– Found that there were heat resistant forms of microbes
• Same year (1876) Ferdinand Cohn discovers heat resistant forms of bacteria called endospores
– Spores can survive in space (Apollo Program,
1960s)
• 1877 Robert Koch demonstrates that anthrax caused by Bacillus anthracis

Major Milestones in Microbiology

Major Milestones in Microbiology

New cells need to be placed in categories
• Aristotle-plant or animal kingdom
• Kingdom Protista (1866)
• Electron microscope (1940 ’ s)
• Kingdom Procaryotae (1968)
• Carl Woese proposed 3 Domains (1978)

Three Domain System

Prokaryotes (Single Celled)
• Bacteria Domain (Eubacteria)
– Peptidoglycan cell walls
• Gram negative
• Gram positive
• Archaea Domain (Archaebacteria)
– Not a peptidoglycan cell wall
– Extremophiles
• Methanogens
• Halophiles
• Thermophiles

Binomial system of nomenclature
• Genus and species
– Escherichia coli, Escherichia coli
– E. coli is not acceptable on exams or unknowns…
• Both names are in italics or underlined and correctly spelled.

Relationship of size and resolution

Types of microscopes
• Brightfield
• Darkfield
• Phase Contrast
• Fluorescent
• Electron

Microscopy-Brightfield

Oil has same refractive index as glass

Microscopy, Oil Immersion
Stained specimen
Wet mount

Microscopy
Electron microscopes - maximum magnification 
100,000X

Microscopy
Electron microscopes - maximum magnification 
100,000X
“ Color-enhanced ”

Relative sizes
Figure: CNX.org

Staining: key to visualization
• Simple
• Differential
• Special

Microscopic Techniques: Dyes and
Staining
•Simple stains
• Stains everything
•Differential stains
• Stain based on cellular traits
Gram stain separates bacteria into two categories based on type of cell wall
Acid Fast Stain – Stains non-peptidoglycan containing bacteria (Mycobacteria)
Gram-positive
Gram-negative

Microscopic Techniques: Dyes and
Staining
•Simple stains
•Differential stains
Gram stain separates bacteria into two categories based on type of cell wall
Purple: Bacteria with high peptidoglycan containing cell walls
Pink: Counter stain

Differential Stain: Acid Fast

Microscopic Techniques: Dyes and
Staining
Fluorescent dyes and tags

Special stain: Capsule Stain

Special stain: Endospore Stain

Special stain: Flagella Stain

Morphology of
Prokaryotic Cells:
Cell Shapes

Morphology of Prokaryotic Cells:
Cell Shapes

Morphology of Prokaryotic Cells:
Cell Groupings

Morphology of Prokaryotic Cells:
Multicellular Associations
Biofilm containing mixed species