Introduction to Microbiology

Unifying Themes
1. The invisible world of microbes underlies and shapes what we call
the "visible world".
2. Microbes have extraordinary genetic and metabolic diversity.
3. Microbial metabolism can create anaerobic environments, and
anaerobic microbes can exploit these environments.
4. Different microbes are adapted to survive and exploit an enormous
range of environments, both inanimate and animate.
5. Among all life forms on earth, microbes have the widest range of
genetic and evolutionary diversity.

The Subject Matter of Microbiology

1. What are microbes?
• Microbes are small organisms, generally smaller than human eye
can detect
• Typical microbes are
o bacteria (in Kingdom Monera)
o protists (in Kingdom Protista)
o algae (in Kingdom Protista or Plantae, depending on
taxonomy)
o fungi (in Kingdom Fungi)
• Note: only members of the Kingdom Animalia (and most Plantae)
are not considered microbes
• Viruses are also considered microbes. Viruses are not cells, but
informational parasite ("piece of bad news wrapped up in
protein"). Viruses are classified separately. Each Kingdom has its
own associated viruses (e.g., HIV virus that causes AIDS cannot
infect bacteria or plants, or for that matter other mammals).
• Many microbes live as single cells or cell clusters; some
multicellular (e.g. filamentous multicells), but not as complex as
animals, plants
2. The Structure of Microbes
Two basic cell architectures: prokaryotes & eukaryotes

Image drawn by Thomas M. Terry for The Biology Place. Used with
permission.

1. Prokaryotes
o "pro" = before, + "karyos" = nucleus
o Includes bacteria and cyanobacteria (formerly blue-green
algae)
o Simple architecture not understood until EM technology in
1940's
o Sample electron micrographs (SLIDES shown in class)
o Typical sizes: 1 um diameter
2. Eukaryotes
o "eu" = true, + "caryos" = nucleus
o Typically contain membrane-bounded organelles (e.g.
mitochondria, lysosomes, endoplasmic reticulum, Golgi
bodies)
o Typical sizes: anywhere from 5 micrometers (yeast cells) to
50 or 100 micrometers. A few cells (such as bird eggs) are
enormous, and some cells (such as animal nerve cells) can
attain lengths of many meters, even though small in
diameter.
o Includes protists, fungi, animals and plants.

3. The variety of Bacteria

• Small variety of bacterial shapes
1. Rods = bacilli (sing. bacillus).
 ƒ View Pseudomonas aeruginosa, a common
opportunistic pathogen and widely distributed soil
bacillus.
ƒ View long bacilli bacteria under the light
microscope (stained slide)
2. Spheres = cocci (sing. coccus).
ƒ View stained Staphylococcus slide.
ƒ Study growth patterns of cocci
3. Spiral forms = spirilla (sing. spirillum).
ƒ View Borrelia burgdorferi, the bacterium that
causes Lyme disesase.
4. Filamentous forms.
ƒ Common among actinomycetes. Many grow in
branching filamentous network called mycelium.
ƒ View actinomycetes
5. Pleiomorphic shapes.
ƒ Some bacteria lack distinct shape; typical of
Mycoplasmas (also called Acholeplasmas). These
organisms lack cell walls, so have no well defined
shape.

6. Square bacteria: discovered 1981, Red Sea shore

(Halophiles)

• Bacterial Nomenclature
o Named by the Linnaean system: Genus + species.
o Examples:
1. Escherichia (genus) coli (species). Named after
Theodor Escherich, German bacteriologist who
discovered this organism in intestinal tract in 1885.
He called it Bacterium coli, but it was subsequently
renamed in his honor.
2. Bacillus megaterium; a large rod shaped organism,
member of the Genus Bacillus.
3. Streptococcus faecalis; fecal organism, member of
the streptococci, a large genus, some members live
in or on animal hosts.
o Name often reveals some characteristic feature.
 o Note: Bacillus (one genus of bacteria, italicized) vs bacilli
(general term for rods, not italicized)

4. History and Distribution of Bacteria

Where do bacteria come from, and where are they found?

1. History
o Earth was formed about 4.5 billion years ago (BYA)
o Fossil bacteria can be found in the oldest rocks (~ 3.8
billion years old)
o Early Earth was anaerobic. Cyanobacteria evolved ability
to use water as raw material in photosynthesis, produced
oxygen gas O2 as waste. This led to buildup of O2 in
atmosphere from 0% to 20% around 2 BYA.
o Eearliest fossil eukaryotes are about 1.5 billion years old,
and animals evolved about 0.6 billion BYA.
o All present-day life evolved from bacteria.
2. Distribution
o Bacteria are the most abundant organisms on earth, found
everywhere; air, water, soil, rocks (live bacteria even found
in rocks more than a mile below earth's surface)
o Billions per gram of fertile soil (will measure this in lab)
14 13
o Humans contain 10 bacterial cells, 10 human cells; 10%
of dry weight of humans is bacterial (mostly in large
intestine). Feces is 1/3 bacteria.
o One of major human problems: getting rid of microbes, or
preventing their growth. Practical problem for food,
beverage, cosmetic, pharmaceutcals, other industries.
o Where are microbes not found? Only inside tissues of
organisms, kept at bay by defensive mechanisms. Even so,
challenges common (cut finger, get infected).

5. What do microbes do?

1. When food is abundant, microbial "behavior" is very simple: EAT,
GROW, AND DIVIDE.
2. Watch movie showing E. coli growing in time-lapse photography
3. Table showing rate of growth of different organims
 Organism Time needed to consume body weight
Human 180 Days
Pig 20 Days
Yeast 30 Minutes
Lactobacillus 10 Minutes
Micrococcus 3 Minutes

4. Growth rates can be phenomenally fast: e.g. some bacteria can

reproduce every 20 min. under optimal conditions. 24 hours, could
have 271 bacteria = 2.4 x 1021. Bacterial cell weighs ca. 10-12 g., so
24 hours growth weighs 2.4 x 1010grams = 2.4 x 107 kg = 26,400
tons.
5. Physiology: what kinds of foods do they eat? How do they extract
energy? Lots of extraordinary tricks: e.g. some bacteria can use up
to 150 different chemicals as the ONLY source of carbon.
Mothballs, starch, etc. Imagine your life if you could do this!
6. Bacteria in animal gut are important for animals to digest food. In
some animals, bacteria are obligatory, animals cannot survive
without them.
7. Many human foodstuffs are produced by bacteria or fungi: yogurt,
cheese, and other sour milk products; saurkraut; beer, wine, and all
other alcoholic beverages; vinegar.
8. Bacteria rarely enjoy continued ample food, so much time spent in
dormant or near-dormant states. Bacteria can survive with minimal
metabolism in very extreme environments, including antarctic ice,
rocks (as far as a mile below earth's surface), boiling sulfur
springs, and more.
9. Bacteria have many sophisticated mechanisms for handling lack of
food, including secreting antibiotics and other toxins ("get rid of
the competition"), modifying intracellular metabolism, and
producing modified structures for dormancy (spores, cysts,
endospores).

6. Why is microbiology important?

1. Disease. Since discovery of infectious microbes, most infectious
diseases controlled by sanitation, preventive medicine, and
chemotherapy.
2. Agriculture. microbes vital in processing materials in soil, e.g.
nitrogen, sulfur, etc.
 3. Food and drink. Microbial fermentations responsible for all
alcoholic beverages, breads, pickles, cheeses, etc. Control of food
and drink spoilage is major concern of food industry.
4. Chemical products. Microbes have incredible variety of
metabolic tricks; can be used to produce acetone and other
commercial solvents, pharmaceuticals, antibiotics, preservatives,
etc.
5. Basic research. Microbes grow fast, produce enormous # of
offspring. Easy to find events that occur only 1 in a billion times if
have 100 billion bacteria in test tube. Crucial to modern biology.
6. Biotechnology. E.g. genetic engineering, ability to move genes
freely from one organism to another, select genes of interest and
amplify their expression. Bacteria are natural hosts for such
activities.

7. How did microbiology become a science?

Major historical figures
• First careful descriptions of microbes by Antony van
Leeuwenhoek (late 1600's) Amateur lens grinder. Made simple
microscope. Drew bacteria, yeasts, etc.
• View micrograph taken through Van Leeuwenhoek's microscope.

Spontaneous Generation controversy.

• From ancient times, belief that live could spring from inert matter
• After Leeuwenhoek, "beasties" believed to arise from water.
• Ex. 1748, Needham boiled mutton broth, sealed container. But
clear broth became cloudy. Conclude: life arose from matter.
• Pasteur (mid 1800's) devised many ingenious expts. to show that
air carried contaminating microbes.
• Expt: Filter air through cotton. Dissolve cotton, look at slide -->
things like spores. Place cotton over sterile (boiled) medium -
filters air, no growth occurs
• Swan neck flask expt.
• Tyndall (late 1800's); provided evidence that some bacteria had
exceptionally heat resistant stage (= endospores).

Microbes cause Disease!

• First shown in plants, early 1800's. Slow to discover human

disease agents
 • Lister (late 1800's); impressed with Pasteur's work, developed
antiseptic surgery; heat sterilize instruments, swab surfaces with
strong acids. Dramatic reduction of post-surgical infections.
• Koch (late 1800's); first demonstrated direct causal link of single
microbe to single disease: Anthrax.
• Koch's postulates: basic logical proof that disease is caused by a
microbe
1. Microbe must be present in every case of disease, but
absent from healthy individuals
2. suspected microbe must be isolated and grown in culture
3. Same disease must result when isolated microbe introduced
into healthy host
4. Same microbe must be isolated again from diseased host

Late 1800's: "Golden Age" of Microbiology.

• Every year, new proof of particular disease caused by particular

microbe: cholera, typhoid, tuberculosis, diphtheria, etc. (see Table
1.2)

Microbes transform organic and inorganic matter

• Pasteur established that microbes cause fermentation, produce

wine, beer, etc.
• Winogradsky (early 1900's) studied soil microbes, showed
bacteria change state of nitrogen, sulfur, iron, carbon. Many can
"eat" inorganic matter, get necessary energy
• Beijerinck (early 1900's) showed root nodules of some plants
contain bacteria that fix nitrogen, produce most ammonia on earth

Recent Developments

• Microbes used in research (fast growth, streamlined genetic

systems, encyclopedic knowledge), easily manipulated. Major role
in molecular biology
• Study of disease continues: new diseases, new problems with old
diseases.
• Microbes important as producers of desired products (eg Pfizer)
• Biotechnology revolution largely dependent on microbes to move
genes around
 MICROORGANISMS AND YOU

MICROORGANISMS AFFECT OUR LIVES: THE GOOD, THE BAD AND THE
UGLY

• Causative agents of diseases and emerging diseases

o AIDS
o Toxic Shock Syndrome
o Lyme Disease
o Bloody diarrhea
• Beneficial Microbes
o Winogradsky & Beijerinck: recycling carbon & nitrogen
o Sewage treatment: recycling water
o Bioremediation: clean up of pollutants
o Biological control: Insect control by microbial toxin
o Traditional Biotechnology (Fermentation, industrial microbiology)
ƒ Sourdough and yoghurt
ƒ Antibiotics, citric acid, lactic acid
o Modern Microbial Biotechnology & Genetic Engineering
ƒ Proteins: IGF, Insulin, GH, interferon, factor VIII, tissue
plasminogen activator, erytropoietin, beta-endorphin
ƒ Vaccines: Hepatitis B, Malaria, influenza
ƒ Improved early diagnostics: monoclonal antibodies
ƒ Gene therapy: Adenosine deaminase cystic fibrosis, muscular
dystrophy
ƒ Genetic improvement in industrial strains
ƒ Agricultural applications: flavor, shelf life, color, texture, damage
protection.
o Importance of Normal microflora
ƒ Protection
ƒ Digestion and energy: ruminants & termites

DEVELOPEMENTS & CONCEPTS IN MICROBIOLOGY

• The golden era of microbiology (1857 - 1914)

o Louis Pasteur
ƒ Life begets life
ƒ Fermentation & sterilization
o Germ theory of disease
ƒ Pasteur & silkworm disease
ƒ Lister
ƒ Semmelweis
o Vaccination
 ƒ Jenner & small pox vaccination
ƒ Pasteur & immunity (virulence & avirulence)
o Chemotherapy & Anibiotics "magic bullets"
ƒ Paul Ehlrich: Salvarsan (arsenic derivative)
ƒ Quinine (bark extract)
ƒ Dye derivatives
ƒ Sulfa- drugs
ƒ Alexander Fleming: Penicillum notatum
ƒ Rene Dubos: B. brevis (gramicidin, tyrocidine) Note: Drug
ressistance & antibiotics
• The modern era of microbiology
o Immunology:
ƒ Lancfield (streptococci & serotying)
o Virology:
ƒ Iwanowski (filterable tobacco mosaic virus)
ƒ Stanley (TMV is different to other cells)
o Recombinant DNA technology:
ƒ Beadle & Tatum: Relationship of gene & enzyme
ƒ Lederberg & Tatum: cojugation
ƒ Watson & Crick: Structure & replication of DNA
ƒ Jacob & Monod: mRNA, gene regulation
ƒ Paul Berg: genes are transferable

History of Microbiology
A Brief History of Microbiology
Development of microscopy:
• Aristotle (384-322) and others believed that living organisms could develop from
non-living materials.
• 1590: Hans and Zacharias Janssen (Dutch lens grinders) mounted two lenses in a
tube to produce the first compound microscope.
• 1660: Robert Hooke (1635-1703) published "Micrographia", containing drawings
and detailed observations of biological materials made with the best compound
microscope and illumination system of the time.
• 1676: Anton van Leeuwenhoek (1632-1723) was the first person to observe
microorganisms.
• 1883: Carl Zeiss and Ernst Abbe pioneered developments in microscopy (such as
immersion lenses and apochromatic lenses which reduce chromatic aberration)
which perist until the present day.
• 1931: Ernst Ruska constructed the first electron microscope.
For a detailed description of the history of light microscopy, click here.

Spontaneous generation controversy:

• 1688: Francesco Redi (1626-1678) was an Italian physician who refuted the idea
of spontaneous generation by showing that rotting meat carefully kept from flies
will not spontaneously produce maggots.
• 1836: Theodor Schwann (1810-1882) helped develop the cell theory of living
organisms, namely that that all living organisms are composed of one or more
cells and that the cell is the basic functional unit of living organisms.
• 1861: Louis Pasteur's (1822-1895) famous experiments with swan-necked flasks
finally proved that microorganisms do not arise by spontaneous generation.
This eventually led to:
• Development of sterilization
• Development of aseptic technique

Proof that microbes cause disease:

1546: Hieronymus Fracastorius (Girolamo Fracastoro) wrote "On Contagion" ("De
contagione et contagiosis morbis et curatione"), the the first known discussion of the
phenomenon of contagious infection.
1835 Agostino Bassi de Lodi showed that a disease affecting silkworms was caused by a
fungus - the first microorganism to be recognized as a contagious agent of animal
disease.
1847: Ignaz Semmelweiss (1818-1865), a Hungarian physician who decided that doctors
in Vienna hospitals were spreading childbed fever while delivering babies. He started
forcing doctors under his supervision to wash their hands before touching patients.
1857: Louis Pasteur proposed the "germ theory" of disease.
1867: Joseph Lister (1827-1912) introduced antiseptics in surgery. By spraying carbolic
acid on surgical instruments, wounds and dressings, he reduced surgical mortality due to
bacterial infection considerably.
1876: Robert Koch (1843-1910). German bacteriologist was the first to cultivate anthrax
bacteria outside the body using blood serum at body temperature. Building on pasteur's
"germ theory", he subsequently published "Koch's postulates" (1884), the critical test for
the involvement of a microorganism in a disease:
1. The agent must be present in every case of the disease.
2. The agent must be isolated and cultured in vitro.
3. The disease must be reproduced when a pure culture of the agent is inoculated
into a susceptible host.
4. The agent must be recoverable from the experimentally-infected host.
This eventually led to:
• Development of pure culture techniques
• Stains, agar, culture media, petri dishes
 Significant Events Of The Last 125 Years
at the
ol 1861
d the
Pasteur introduced the terms aerobic and anaerobic in describing the growth of
yeast at the expense of sugar in the presence or absence of oxygen. He
ompt. observed that more alcohol was produced in the absence of oxygen when
sugar is fermented, which is now termed the Pasteur effect.

Pasteur, L. "Animalcules infusoires vivant sans gaz oxygene libre et determinant des
fermentations." Compt. Rend. Acad. Sci. (Paris) 52:344-347, 1861

1870

Thomas H. Huxley's Biogenesis and Abiogenesis address is the first clear

statement of the basic outlines of modern Darwinian science on the question of
the origin of life. The terms "biogenesis" (for life only from pre-existing life) and
"abiogenesis" (for life from nonliving materials, what had previously been called
spontaneous generation) as used by Huxley in this speech have become the
standard terms for discussing the subject of how life originates. The speech
offered powerful support for Pasteur's claim to have experimentally disproved
spontaneous generation. The speech was also Huxley's attempt to define an
orthodox Darwinian position on the question, and attempt to define as "non-
Darwinian" all those Darwin supporters who believed that spontaneous
generation up to the present day was an essential requirement of evolutionary
science. Henry Charlton Bastian was the most prominent leader of that faction
of Darwinians, though Huxley was so successful in defining them out of the
story that very few people today even realize that there WERE Darwinians who
were serious, talented evolutionary scientists, yet also thought a biogenesis
was necessary in evolution up to the present day.

1872

Ferdinand J. Cohn contributes to the founding of the science of

bacteriology. In the publication Ueber Bakterien, he discusses the
role of microorganisms in the cycling of elements in nature. In
1875, Cohn will publish an early classification of bacteria, using
the genus name, Bacillus, for the first time.

Cohn, F. 1872. Ueber Bakterien, die kleinsten lebenden Wesen. Lüedritz’sche

Verlagsbuchhandlung Carl Habel, Berlin.
Significant Events Of The Last 125 Years

1861

Pasteur introduced the terms aerobic and anaerobic in describing the growth of yeast at the
expense of sugar in the presence or absence of oxygen. He observed that more alcohol was
produced in the absence of oxygen when sugar is fermented, which is now termed the
Pasteur effect.

Pasteur, L. "Animalcules infusoires vivant sans gaz oxygene libre et determinant des fermentations." Compt.
Rend. Acad. Sci. (Paris) 52:344-347, 1861

1870

Thomas H. Huxley's Biogenesis and Abiogenesis address is the first clear statement of the
basic outlines of modern Darwinian science on the question of the origin of life. The terms
"biogenesis" (for life only from pre-existing life) and "abiogenesis" (for life from nonliving
materials, what had previously been called spontaneous generation) as used by Huxley in this
speech have become the standard terms for discussing the subject of how life originates. The
speech offered powerful support for Pasteur's claim to have experimentally disproved
spontaneous generation. The speech was also Huxley's attempt to define an orthodox
Darwinian position on the question, and attempt to define as "non-Darwinian" all those Darwin
supporters who believed that spontaneous generation up to the present day was an essential
requirement of evolutionary science. Henry Charlton Bastian was the most prominent leader
of that faction of Darwinians, though Huxley was so successful in defining them out of the
story that very few people today even realize that there WERE Darwinians who were serious,
talented evolutionary scientists, yet also thought a biogenesis was necessary in evolution up
to the present day.

Biogenesis and Abiogenesis

James Strick. 1999. Darwinism and the Origin of Life: the Role of H.C. Bastian in the British Spontaneous
Generation Debates, 1868-1873. Journal of the History of Biology, 32:1-42 [PDF]
 1872

Ferdinand J. Cohn contributes to the founding of the science of bacteriology. In

the publication Ueber Bakterien, he discusses the role of microorganisms in the
cycling of elements in nature. In 1875, Cohn will publish an early classification of
bacteria, using the genus name, Bacillus, for the first time.

Cohn, F. 1872. Ueber Bakterien, die kleinsten lebenden Wesen. Lüedritz’sche

Verlagsbuchhandlung Carl Habel, Berlin.

Cohn, F., 1875. Untersuchungen ueber Bakterien. Beitraege zur Biologie der Planzen 1:127-222
In Milestones in Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p210
[PDF]

Ferdinand Cohn, a Founder of Modern Microbiology, ASM News 65. 1999.p.547

The German botanist Brefeld reported growing fungal colonies from single spores on gelatin
surfaces. Prior to this innovation that resulted in the isolation of pure culture of
microorganisms, pigmented bacterial colonies were isolated by the German biologist
Schroeter on slices of potato incubated in a moist environment.

Brefeld, O. Botanische Untersuchungen uber Schimmelpilze, Heft I, Mucor mucedo, Chaetocladium Jones ii,
Piptocephalis Fresiana: Zygomyceten, Leipzig, 1872.

Schroeter, J. "Ueber einige durch Bacterien gebildete Pigmente." Beitr. Z. Biol. D. Pflanzen 1:2, 109-126.

1876

Robert Koch publishes a paper on his work with anthrax, pointing explicitly to
a bacterium as the cause of this disease. This validates the germ theory of
disease. Prior, in 1872, he was approved as a district medical officer in
Poland where he discovered anthrax was endemic. His work on anthrax was
presented and his papers on the subject were published under the auspices
of Ferdinand Cohn.

Koch, R. 1876. Untersuchungen ueber Bakterien V. Die Aetiologie der Milzbrand-Krankheit, begruendent auf die
Entwicklungsgeschichte des Bacillus Anthracis. Beitr. z. Biol. D. Pflanzen 2: 277-310. In Milestones in
Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p89 [PDF].

1877
APPLICATIONS OF PROCARYOTES IN INDUSTRY AND BIOTECHNOLOGY

In addition to other ecological roles, procaryotes, especially bacteria, are used

industrially in the manufacture of foods, drugs, vaccines, insecticides, enzymes,
hormones and other useful biological products. In fact, through genetic engineering of
bacteria, these unicellular organisms can be coaxed to produce just about anything that
there is a gene for. The genetic systems of bacteria are the foundation of the
biotechnology industry.

In the foods industry, lactic acid bacteria such as Lactobacillus and Streptococcus are
used the manufacture of dairy products such as yogurt, cheese, buttermilk, sour cream,
and butter. Lactic acid fermentations are also used in pickling process. Bacterial
fermentations can be used to produce lactic acid, acetic acid, ethanol or acetone. In
many parts of the world, various human cultures ferment indigenous plant material using
Zymomonas bacteria to produce the regional alcoholic beverage. For example, in
Mexico, a Maguey cactus (Agave) is fermented to "cactus beer" or pulque. Pulque can
be ingested as is, or distilled into tequila.
In the pharmaceutical industry, bacteria are used to produce antibiotics, vaccines, and
medically-useful enzymes. Most antibiotics are made by bacteria that live in soil.
Actinomycetes such as Streptomyces produce tetracyclines, erythromycin, streptomycin,
rifamycin and ivermectin. Bacillus species produce bacitracin and polymyxin. Bacterial
products are used in the manufacture of vaccines for immunization against infectious
disease. Vaccines against diphtheria, whooping cough, tetanus, typhoid fever and
cholera are made from components of the bacteria that cause the respective diseases. It
is significant to note here that the use of antibiotics against infectious disease and the
widespread practice of vaccination (immunization) against infectious disease are two
twentieth-century developments that have drastically increased the quality of life and the
average life expectancy of individuals in developed countries.

The biotechnology industry uses bacterial cells for the production of human hormones
such as insulin and human growth factor (protropin), and human proteins such as
interferon, interleukin-2, and tumor necrosis factor. These products are used for the
treatment of a variety of diseases ranging from diabetes to tuberculosis and AIDS. Other
biotehnological applications of bacteria involve the genetic construction of "super strains"
of organisms to perform a particular metabolic task in the environment. For example,
bacteria which have been engineered genetically to degrade petroleum products can be
used in cleanup efforts of oil spills in seas or on beaches. One area of biotechnology
involves improvement of the qualities of plants through genetic engineering. Genes can
be introduced into plants by a bacterium Agrobacterium tumefaciens. Using A.
tumefaciens, plants have been genetically engineered so that they are resistant to
certain pests, herbicides, and diseases. Finally, the polymerase chain reaction (PCR), a
mainstay of the biotechnology industry because it allows scientists to duplicate genes
starting with a single molecule of DNA, is based on the use of a DNA polymerase
enzyme derived from a thermophilic bacterium.