Chapter 1: Introduction to Microbiology

Chapter 1: Introduction to Microbiology

Question to Ponder!
Advertisements tell you that bacteria and viruses are all over your home and that you need to
buy antibacterial cleaning products. Should you?

Types of Microorganisms

Microbes: Tiny but Mighty

Microbiology – specialized area of biology that deals with living things too small to be seen
without magnification.

Microorganisms include:
 Bacteria
 Archaea
 Protozoa
 Fungi
 Helminths
 Viruses
 Algae

What do they have in common? How are they different from one another?

Evolutionary Timeline

 Microbes have shaped the development of earth’s habitat for billions of years.
 (Earth is about 4.6 billion years old)
 Single-celled organisms appeared on this planet about 3.8 billion years ago.
 Three cell types arose from a single (extinct) common ancestor:
 Eukaryotes – “true nucleus”
 Bacteria – single-celled, no true nucleus
 Archaea – single-celled, no true nucleus, distinct from bacteria

BACTERIA
 Prokaryotic (has no nucleus)
 Cell wall with peptidoglycan (peptide = protein + glycan = sugar) (most)
 Unicellular (meaning one cell)
 Reproduces by binary fission (asexually)
 Circular DNA
 Some are photosynthetic (autotrophic) (e.g., Cyanobacteria found in water), others are
heterotrophic.

ARCHAEA

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 Prokaryotic
 Cell wall lacks peptidoglycan (pseudomurein instead, it is still protein and sugar mix
but it’s not chemically the same as the peptidoglycan)
 Unicellular
 Reproduces by binary fission.
 Circular DNA
 Extremophiles: (-phile meaning “lover’)
 Thermophiles (heat lover)
 Halophiles (salt lover)
 Methanogens (produce methane as a waste product of respiration)

FUNGI
 Eukaryotic (has nucleus)
 Cell wall has chitin (polysaccharide = many sugars)
 Heterotrophic (molds usually found in dark damp places, which means they are not
likely to be photosynthetic (saprobe = feeds on dead decaying matter)
 Unicellular (yeast) or multicellular (bread molds and mushrooms)
 Can reproduce sexually or asexually.
 Linear DNA

**Saccharomyces cerevisiae – literally means sugar fungus that makes beer; type of yeast that
is used to make beer, bread and wine through fermentation.

PROTOZOA
 Eukaryotic
 Usually lacks cell walls.
 Usually heterotrophic.
 Unicellular
 Can reproduce sexually or asexually.
 Moves by:
 Pseudopods
 Flagella
 Cilia
 Some are non-motile.

**Trypanosoma – an organism that can cause African Sleeping Sickness, when patients have
this infection and the infection is heavy meaning there’s a lot of these organisms in the blood,
the organisms are then taking the host food.

ALGAE
 Eukaryotic
 Cell wall has cellulose (polysaccharide)
 Photosynthetic (autotrophic or self-feeders)
 Unicellular or multicellular

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 Can reproduce sexually or asexually.

 Often contains pigments: green, red, or brown.

VIRUSES
 Acellular (not made of cells meaning non-living)
 Obligate intracellular parasites (obligate means it has to be with in a cell; viruses cannot
reproduce without a host cell)
 DNA or RNA but not both
 May be enveloped or naked.
 A capsid (protein coat) is required.

MULTICELLULAR ANIMAL PARASITES

 Helminths = flat worms and round worms
 No cell wall.
 Heterotrophic
 Can reproduce sexually or asexually.
 Have microscopic stages.

Which of the following is NOT a characteristic of bacteria?

A. Are prokaryotic
B. Have peptidoglycan cell walls
C. Are multicellular
D. Reproduce by binary fission
E. Have the ability to move

Comparison of Organisms
Compare and contrast the various types of organisms.
Bacteria Archaea Fungi Protozoan Algae Helminth
Prokaryotic
or
Eukaryotic
Cell wall
composition
Heterotroph
or
Autotroph
Unicellular
or
multicellular
Asexual or
sexual
reproductio
n

MICROBES IN OUR LIVES

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How do microorganisms affect our everyday lives?

The Nature of Microorganisms

 Microbes are very easy and very difficult to study:
 Reproduce rapidly (e.g. E.coli reproduce every 20 minutes)
 Can be grown in large populations in the laboratory
 Cannot be seen directly
 Analyzed though indirect means
 Viewed through microscopes
 Microbes are Ubiquitous (found everywhere) and are found:
 Deep in the earth’s crust
 In polar ice caps and oceans
 Inside the bodies of plants and animals
 In the earth’s landscape
 Essential to life (microbiomes—types of bacteria found in our body—our bodies
do not function properly without the help of those microbes)

Photosynthesis
 Photosynthesis:
 Light-fueled conversion of carbon dioxide to organic material
 Accompanied by the formation of oxygen.
 Anoxygenic photosynthesis:
 Occurred in bacteria before plants evolved.
 Did not produce oxygen.
 More efficient in extracting energy from sunlight
 Oxygenic photosynthesis:
 Evolved from anoxygenic photosynthesis.
 Photosynthetic microorganisms are responsible for 70% of the earth’s
photosynthesis.

How Microbes Shape Our Planet

 Microorganisms are the main forces that drive the structure and content of the soil,
water, and atmosphere:
 Microbes produce CO2, NO, and CH3 that insulate the earth’s atmosphere
 Microorganisms are the most abundant cellular organisms in the oceans
 Viruses are the most abundant inhabitants of the oceans.
 Bacteria and fungi live in close associations with plants and assist them in obtaining
nutrients and water and may protect them against disease.

Microbes and Humans

 Historical uses of microbes by humans:
 Bread production (yeast help the dough rise because it produces CO 2)
 Alcohol production
 Cheese production

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 Treatment of wounds and lesions (produce antibiotics)

 Mining precious metals
 Cleaning up human-created contamination (oil-spill - there are bacteria that naturally
can consume/digest and break up the oil)

Biotechnology
 Genetic engineering:
 Manipulates the genetics of microbes, plants, and animals for the purpose of
creating new products and genetically modified organisms (GMOs)
 E.g. they can be used to change the DNA of a plant for example to make that plant
to be more resistant to a particular pest.
 Recombinant DNA technology:
 Makes it possible to transfer genetic material from one organism to another and
deliberately alter DNA.
E.g. the first human recombinant drug to be produced called Humulin (human
insulin) way back in the 80s. For patients who are diabetic (type 1 diabetes, juvenile
diabetes), they have an autoimmune disease.

Watch the short clip about recombinant DNA technology: https://www.youtube.com/watch?

v=OpU_CQ0pFyQ

 Bioremediation:
 Uses microbes already present or introduced intentionally to restore stability or clean
up toxic pollutants.

Microbes Harming Humans

 The vast majority of microorganisms that associate with humans are harmless or
beneficial.

 Pathogens - microbes that cause disease:

 Over 2,000 different microbes cause disease.
 Ten billion infections occur across the world every year
 Infectious diseases are among the most common causes of death worldwide.

Microbes and Disease

 Emerging and reemerging diseases:
 COVID!! (SARS, MERS-Middle Eastern Respiratory Syndrome)
 AIDS
 Hepatitis C
 Zika virus (associated with mosquitoes)
 West Nile virus
 Tuberculosis
 Associations between noninfectious diseases and microbes:
 Gastric ulcers are caused by Helicobacter pylori.

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 Multiple sclerosis, OCD, coronary artery disease, and obesity have been linked to
chronic infections with microbes.

Infectious Disease Trends

 Increasing number of patients with weakened defenses:
 Subject to infections by common microbes that are not pathogenic to healthy people
(opportunistic pathogen).
 Increase in microbes that are resistant to drugs.
e.g. gonorrhea (STI) – historically was relatively easy to treat, got gonorrhea took an
antibiotic, problem solved. However, multi-drug resistant strains of Neisseria gonorrhea
are emerging. So what was once an easy to treat STI is now very difficult to treat
because the bacteria has become resistant to many of our antibiotics.

NAMING AND CLASSIFYING MICROORGANISMS

Naming, Classifying, and Identifying Microorganisms

 Taxonomy: the science of classifying living things.
 Nomenclature: the assignment of scientific names to the various taxonomic categories
and to individual organisms.
 Classification: the orderly arrangement of organisms into a hierarchy.
 Identification: the process of discovering and recording traits of organisms so they
can be placed in an overall taxonomic scheme.

Nomenclature
 Nomenclature (naming) of organisms
 Established in 1735 by Carolus Linnaeus
 Latinized
 Binomial Nomenclature: Each organism has two names:
1) Genus
 1st, Capitalized.
2) Specific Epithet (species)
 2nd, Lower case
 Both names are underlined (separately) or italicized (if typed)

Scientific Names
 May be descriptive or honor a scientist.
 Escherichia coli
 Honors the discoverer, Theodor Escherich
 Describes the bacterium’s habitat.
 Staphylococcus aureus
 Describes the clustered (staphylo-) spherical (cocci) cells.
 Describes the gold-colored (aureus) colonies.
 After the first use, scientific names may be abbreviated with the first letter of the genus
and the specific epithet:

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 Escherichia coli and Staphylococcus aureus are found in the human body. E. coli is
found in the colon, and S. aureus is skin.

Classification – 3 Domains
 1978: Carl Woese
 Classified by rRNA (RNA found in ribosome to produce proteins) analysis
 (compare sequences of rRNA, the more in common, meaning the more similarities in
their sequences, the more closely related they are; the greater the number of
differences in the rRNA that means that those organisms are more diverse, they’re
more distinct and they evolved from each other a lot longer ago in our evolutionary
history)
1) Bacteria (prokaryotic)
2) Archaea (prokaryotic)
3) Eukarya (eukaryotic)
Includes: (Kingdom System)
Protists (slime molds, algae, protozoa)
Fungi (mold, mushroom, yeast)
Plants (mosses, ferns, conifers, flowering plants)
Animals (humans, dogs, monkey, octopus, insects, coral, sea star)

Classification
 Organized into several descending ranks, beginning with the most general and ending
with the smallest and most specific:
 Domain
 Kingdom
 Phylum or Division
 Class
 Order
 Family
 Genus
 Species – a group of individuals that have the ability to breed and produce fertile
offspring.
Mnemonic Device (Do Keep Pots Clean Or Family Gets Sick)

Classifying Living Things

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A Brief History of Microbiology

The First Observations

 Ancestors of bacteria were the first life on Earth.
 1665: Robert Hooke reported that living things were composed of little boxes or “cells”
from looking at cork
 Led to the cell theory: All living things are composed of cells and come from
preexisting cells.
-also studied household objects, plants, trees and he described cellular structures
and drew sketches of little structures that seemed to be alive
 1673-1723: Anton van Leeuwenhoek described live microorganisms (“animalcules”)
-he looked at different specimens like rain water, feces, scrapings from teeth

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1673-1723: Anton van Leeuwenhoek was likely the first to observe live microbes through the more than 400
microscope he constructed. He wrote about "animalcules" and made detailed drawings of the organisms he was
seeing. (Tortora, Page 7)
Source: https://www.sutori.com/en/item/1673-1723-anton-van-leeuwenhoek-was-likely-the-first-to-observe-live-
microbes-t

The Debate over Spontaneous Generation

 Spontaneous generation: The hypothesis that living organisms arise from nonliving
matter; a “vital force” forms life (non-living to living)
 Biogenesis: The hypothesis that the living organisms arise from preexisting life (living
to living)

Evidence Pro and Con

 1668: Francesco Redi (Italian physician) – Maggots don’t arise from decaying meat

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- Helped provide evidence in support of biogenesis.

- Note: In any scientific theory, you can’t prove any scientific theory. You can provide
evidence in support of a particular theory, you can provide evidence to falsify another
what we call an alternative hypothesis etc. But we can’t ever prove a theory. We can
just say that the alternate hypothesis is not possible.
- In this case, it is basically ruling out spontaneous generation.

Evidence Pro and Con

 1745: John Needham (Englishman) boiled nutrient broth

-experimental design was flawed! Because he capped it after boiling, so bacteria already
had a chance to fall in after the broth was boiled.

Evidence Pro and Con

 1765: Lazzaro Spallanzani (Italian scientist) – Needham should have covered before
boiling (microbes from air)

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Evidence Pro and Con

 1861: Louis Pasteur Results of S-shaped Flask Experiment
 Microbes in air, can contaminate.
 Air does not create microbes.
 Disproved spontaneous generation.
 Credited with aseptic technique (techniques that prevent contamination by unwanted
microorganisms)

Source: https://www.timetoast.com/timelines/sciences-vs-time

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**Which of the following statements is the best definition of biogenesis?

A) Nonliving matter gives rise to living organisms.
B) Living cells can only arise from preexisting cells.
C) A vital force is necessary for life.
D) Air is necessary for living organisms.
E) Microorganisms can be generated from non-living matter.

The Golden Age of Microbiology

 1857-1914
 Rapid advances by Pasteur and Robert Koch
 Microbiology established as science.

Fermentation and Pasteurization

o Pasteur
 Why did beer/wine sour?
 Yeast converts sugar to alcohol without air (fermentation).
-if you grow yeasts in anaerobic conditions they will do
alcoholic fermentation and they will produce alcohol;
however, if that wine for example or beer is exposed to air
the alcohol is then converted to acetic acid by bacteria
 With air, alcohol is converted to acetic acid by bacteria.

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 Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not
hot enough to evaporate the alcohol in wine.
 Pasteurization is the application of a gentle heat for a short time.
-Gentle heat kills most bacteria

The Germ Theory of Disease

 1840s: Ignaz Semmelweis (Hungarian physician)
- Childbirth fever from septicemia (bacteria in the blood) was higher for physicians than
for midwives
- Advocated handwashing between patients
- Incidence dropped from 35% to 1%
- committed to an asylum and died after being admitted by a beating by a guard

-doctors/physicians are considered superior people during those times, they are
considered clean; they will examine/dissect cadavers (autopsy) in the morning and
deliver babies in the afternoon

The Germ Theory of Disease

 1860s: Joseph Lister (Surgeon)
 Applied germ theory to medical practices.
- Cleaned instruments between surgeries
- Knew phenol (carbolic acid) killed bacteria
- Used carbolic acid as chemical control agent (to disinfect the surgical equipment
between the surgeries)

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The Germ Theory of Disease

 1875: Robert Koch
- German physician
- Koch’s postulates are a series of logical steps that establish whether or not an
organism is pathogenic and which disease it caused
- Proved bacteria cause disease
- Germ theory of disease
- Discovered Bacillus anthracis from a cow that died of anthrax

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Vaccination
 1796: Edward Jenner
- 1st vaccine
- No smallpox in milkmaids/cowpox
- Exposed individual to material from cowpox lesion
- Then exposed to smallpox, no infection
- The protection from disease provided by vaccination is called immunity.

**Cowpox is similar to, but much milder than, the highly contagious and often deadly
smallpox disease. Its close resemblance to the mild form of smallpox and the
observation that dairy farmers were immune to smallpox inspired the modern smallpox
vaccine, created and administered by English physician Edward Jenner.

 1880: Pasteur
- Discovered why vaccinations work
- Cholera bacterium lost ability to cause disease after grown in the lab for long periods
- Still able to induce immunity

A Fortunate Accident - Antibiotics

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Recent Advances in Microbiology

Disocvery of Restriction Enzymes – 1970s

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The Invention of the PCR Technique – 1980s

The Importance of Small RNAs – 2000s

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Genetic Identification of the Human Microbiome – 2010s and Beyond

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