01.

Microbiology

Microbiology is the Study of Organisms too small to be seen clearly with the
unaided Eye.
Bacteriology is the Study of Bacteria (G= rods) [Singular = Bacterium]
• Bacteria are Prokaryotes (G= before a kernel [nucleus]) whose Shapes are
determined by a uniquely structured Cell Wall
Bacteria are always included in a Microbiology Course. In fact, many Microbiology
Courses are essentially Bacteriology Courses.

• The overwhelming Majority of Bacteria are Soil-dwelling Organisms

- We'll be working with two Soil Bacteria:
• Bacillus cereus (Bacillus cereus)
Bacillus cereus is a Gram Positive Rod (or Bacillus).

• Pseudomonas putida (Pseudomonas putida)

Pseudomonas putida is a Gram Negative Rod (or Bacillus)
Most Bacteria are vitally important in Biodegradation and in Biogeochemical Cycles.
Plants and Animals have been dying for Billions of Years. Were it not for Bacteria
(and Fungi), enormous Amounts of Organic Matter would be tied up in this Biomass.

• Some Bacteria live in us or on us

- We'll be working with four Bacteria associated with us
Two of these are Skin Bacteria
Micrococcus luteus (Micrococcus luteus)
Micrococcus luteus is a Gram Positive Sphere (or Coccus)

Staphylococcus epidermidis (Staphylococcus epidermidis)

Staphylococcus epidermidis is a Gram Positive Sphere (or Coccus)

Good Bacteria on our Skin prevent Bad Bacteria from taking up Residence.

Two of these are Enteric (Intestinal) Bacteria

Enterobacter aerogenes (Enterobacter aerogenes)
Enterobacter aerogenes is a Gram Negative Rod (or Bacillus)

Escherichia coli or E. coli (Escherichia coli or E. coli)

E. coli is a Gram Negative Rod (or Bacillus)

Good Bacteria in our Intestine help with Digestion and synthesize Vitamins.

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The Shape of Bacterial is determined by their unique Cell Wall
• Cocci (G= berries) [Singular = Coccus]
- Spherical
Coccus is the Default Shape for Bacteria. Other Shapes (Bacillus, Vibrio)
require additional Genes.

• Diplococci (G= two berries) [Singular = Diplococcus]

- Two Spheres
• Streptococci (G= knotted berries) [Singular = Streptococcus]
- Strings of Spheres
Each Cell Division occurs in the same Plane. (Bacteria know Geometry!)

• Staphylococci (G= bunch of berries) [Singular = Staphylococcus]

- Clusters of Spheres
Each Cell Division can (and does) occur in a different Plane.

• Sarcinae (L= bundle) [Singular = Sarcina]

- Cubes of Spheres
(1) Each Cell divides. (2) The Plane of Cell Division shifts horizontally 90°
and each Cell Divides again forming a Tetrad of four Cells. (3) The Plane of
Cell Division shifts vertically 90° and each Cell Divides again forming a Cube
of eight Cells. Sarcina look like Borg Cubes.

• Bacilli (G= rod) [Singular = Bacillus]

- Rods
• Vibrios (L= to vibrate) [Singular Vibrio]
- Comma-shaped
• Spirilla (L= spiral) [Singular = Spirillum]
- Rigid Spirals (technically, Helices)
• Spirochetes (L= spiral + G= hair) [Singular = Spirochete]
- Flexible Spirals (again, technically Helices)
if you know a Friend who regularly cheats on their Significant Other, you are
aware of your Friend's flexible Code of Ethics.
A Spiral is a Structure that winds in a continuously widening or tightening
Diameter (the Groove on a Vinyl LP or a Watch Spring is a Spiral).
A Helix is a Structure that winds in a constant Diameter, resulting in a Three-
Dimensional Shape like a Wire wound around a Cylinder. The DNA Model in
the Life Sciences Building Entry Stairwell is a Helix.

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The Growth of Bacteria in the Lab

• Incubate (L= to lie upon)

- To maintain ("grow") a Culture at a specific Temperature for Growth
Not surprisingly, our MIC 103L Bacteria like to grow at a warmish Room
Temperature (30°C) or at Warm-Blooded Animal Temperature (37°C)

• Pure Culture
- A Population of Cells arising from a single Cell
Pure Culture is the sine quo non (L= without this nothing) of Microbiology.

• Colony (L= settlement)

- A visible Growth or Cluster of Microbes on a Solid Medium
A Colony represents a Pure Culture (or Clone)

Plate Media
There are several different Types of Agar we’ll be routinely using in MIC 103L. Some are
identifiable by their unique Color; others are marked with a colored Strip on the Side.

• Nutrient Agar (Black Stripe)

Nutrient Agar, our All-Singing, All-Dancing Medium, contains a bit of Beef Extract.
Just about anything will grow reasonably well on Nutrient Agar.

• Yeast, Glucose, Calcium Carbonate Agar / YGC Agar (Red Stripe)

YGC Agar is the Medium that we use for our Skin Bacteria Micrococcus luteus,
and Staphylococcus epidermidis, and for our Food Bacterium Streptococcus lactis.
It looks like White Chocolate because the Calcium Carbonate won’t go into Solution
unless the Medium is Acidic.

• Sodium Benzoate Agar (Green Stripe)

Sodium Benzoate Agar is used to select for Pseudomonas sp., a Bacteriaum that can
utilize the synthetic Compound Sodium Benzoate as a Carbon Source.

• Fluorescence Agar / F Agar (Brown Stripe)

F Agar is a low Iron Medium. When Pseudomonas sp. are grown on F Agar they
secrete characteristic fluorescent Compounds (Siderophores).

• Eosin-Methylene Blue Agar / EMB Agar (Dark Burgundy Color Agar)

EMB Agar is used to distinguish E. coli and Enterobacter aerogenes. Colonies of
E. coli will be Purple, surrounded by a Fly-Butt Green Metallic Sheen. Colonies of
Enterobacter aerogenes will be Pepto Bismol Pink.

• MacConkey Agar (Light Burgundy Color)

MacConkey Agar contains Bile Salts and Crystal Violet that inhibit the Growth of
Gram Positive Bacteria and select for the Growth of Enteric Bacteria.

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 Temperature and Bacterial Growth
Bacteria are Poikilotherms/Ectotherms; their Internal Temperature is the same as their
Surroundings. At the Minimal Temperature the Plasma Membrane gels and Transport
ceases; at the Maximum Temperature Proteins and Nucleic Acids denature.

• Psychrophile (G= cold loving)

- Optimum Growth at or below 20°C
- Cell Membranes have lots of Unsaturated Fatty Acids
Psychrophiles are common in your Refrigerator (04°C) and are a very real Problem
for the Food Industry. They are common in expected Areas like the Arctic, the
Antarctic and Mountains. Somewhat surprisingly, they are also common on the
Ocean Floor (where the average Temperature is a surprising 02°C).

• Mesophile (G= middle loving)

- Optimum 25°C to 40°C
- Most Bacteria
- Most Pathogens
• Thermophile (G= heat loving)
- Optimum 50°C to 60°C (with a few near 100°C)
- Cell Membranes have lots of Saturated Fatty Acids
Thermophiles are found in Compost Heaps and Hot Springs. Some are found in Hot
Water Lines of Powerplants and Nuclear Reactions. A few are found near Deep
Ocean Vents. The Enzyme Taq Polymerase, produced by the Obligate Thermophile
Thermus aquaticus, is vital to the Polymerase Chain Reaction (PCR).

Oxygen and Bacterial Growth

In his Short Story “Report on Planet Three” Arthur C. Clark wrote a Scientific Report by
Intelligent Aliens debating the Possibility of Life on Earth. One of their Strongest Arguments
against Life on this Planet is that it has an Atmosphere containing the extremely Reactive and
Corrosive Element Oxygen.

• Aerobe
- Require O2 for Growth
• Anaerobe
- Do not require O2 for growth
Some Anaerobic Environments are a bit surprising. The Bottom of a Pond or a Bog is
almost always Anaerobic. The Human Gut is also Anaerobic, as is the Surface of
your Teeth, between the Enamel and all the Plaque. And most Wounds become at
least partially Anaerobic as a result of the Decay of Dead Tissue.

NOTE: The Adjective "Obligate" ("must be") or "Facultative" ("could be") sometimes precedes these
Growth Categories. An Obligate Thermophile must be incubated at High Temperature. A Facultative
Anaerobe could be incubated without Oxygen but would grow better in its Presence.

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Eukaryotes and Prokaryotes

Animals, Plants and Protozoa are Eukaryotes. Bacteria are Prokaryotes. Think
of Eukaryotes as iMac 27-Inch Retinas (massive and awesomely powerful).
Think of Prokaryotes as iPhones (small and surprisingly powerful). Neither is
inherently superior to the other.
Eukaryotes (G= true kernel [nucleus])
Eukaryotes such as Protozoa have a Membrane-bounded Nucleus and
Membrane-bounded Organelles (L= little organs).
A Eukaryotic Cell is like Downton Abbey, with lots different Rooms for each Function:
Kitchen, Pantry, Scullery, Dining Room, Breakfast Room.....

• A Typical Eukaryotic Cell measures approximately 10 to 30 µm.

A large Pumpkin or a large Watermelon measures ~30 Inches.

• The Nucleus archives and copies Genetic Information

- Replication and Transcription occur in the Nucleus
- A Typical Nucleus measures about 3 µm
A Tangerine measures about 3 Inches.

• Ribosomes synthesize Proteins

- Translation occurs on 80S Ribosomes ("S" = Svedberg Unit)
Svedberg Units are a Centrifugation Coefficient named after the Swedish
Chemist Theodor Svedberg who invented the Ultracentrifuge.

- A Typical Eukaryotic Ribosome measures about 0.03 µm

Course Sand has a Particle Diameter of about 0.03 Inches.
"Free" Ribosomes lead a free-floating Existence in the Cytoplasm. These
Ribosomes synthesize Proteins that will remain in the Cytoplasm.
Many Ribosomes are associated with a the Endoplasmic Reticulum or ER
(G= network in the cytoplasm). These Ribosomes synthesize Proteins that will
be exported from the Cytoplasm into Organelles or out of the Cell

• Mitochondria generate Energy from Food (Respiration).

A Typical Mitochondrion measures 0.5 x 1.0 µm
A Cashew measures about 0.5 x 1.0 Inch.

• Chloroplasts generate Energy from Light (Photosynthesis).

- A Typical Chloroplast measures 4 to 6 µm
A Mango measures about 4 to 6 Inches.

• The Cell Membrane is a characteristic Lipid Bilayer (L= two layers)

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Prokaryotes (G= before a kernel [nucleus])
Prokaryotes do not have a Membrane-bounded Nucleus or Organelles
• A Typical Bacterium measures approximately 1.5 x 4 µm.
A PowerBar measures about 1.5 x 4 Inches.

• Bacteria do not have Membrane-bounded Organelles

Bacteria are like Dorm Rooms or Studio Apartments. Everything occurs within the
same Space. You might have a Site for your Computer and a Site for your
Microwave and Refrigerator but it's all in the same Room.

• Bacteria have a unique Cell Wall

- The Cell Wall determines and maintains the Shape of Bacteria

• A Major Component of the Bacterial Cell Wall is the Polymer
Peptidoglycan (also called Murein [L= wall])
• Peptidoglycan is unique to Bacteria
Animals and Plants do not have Cell Walls composed of
Peptidoglycan. This will be Important when we discuss the Modes of
Action of Antibiotics in Lecture 5.

• The Nucleoid (G= like a kernel [nucleus]) archives and Copies

Genetic Information

• Ribosomes synthesize Proteins

- Translation occurs on smaller 70S Ribosomes ("S" = Svedberg Unit)
- A Typical Bacterial Ribosome measures about 0.02 µm
Fine Sand has a Particle Diameter of about 0.02 Inches.
Replication, Transcription and Translation can occur almost simultaneously
in Bacteria. Transcription and Translation frequently occur in Tandem.
Animals and Plants do not have 70S Ribosomes in their Cytoplasm but their
Mitochondria and Chloroplasts have 70S Ribosomes. This will be Important
when we discuss the Modes of Action of Antibiotics.

• The Cell Membrane is a characteristic Lipid Bilayer.

-- In some Bacteria it generates Energy from Food (Respiration)
Such Bacteria function suspiciously similarly to Mitochondria.

-- In some Bacteria it generates Energy from Light (Photosynthesis)

Such Bacteria function suspiciously similarly to Chloroplasts.

The Total Biomass of Prokaryotes on this Planet exceeds the Total Biomass
of Eukaryotes on this Planet. We're essentially "Planet Prokaryote".

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