CHAPTER 1: The Evolution of Microorganisms and Microbiology

- Because not all “prokaryotes” are the same

and therefore should not be grouped
together in a single kingdom.
- Currently argued that the term prokaryote is
not meaningful and should be abandoned.
Great progress
(1) Learned about the detailed structure of
microbial cells from the use of electron
microscopy.
(2) Microbiologists have determined the
biochemical and physiological
characteristics of many different
microorganism
Microorganisms – organisms and acellular biological (3) Sequences of nucleic acids and protein from
entities too small to be seen clearly by the unaided a wide variety of organism have been
eye compared.

- 1 millimeter or less in diameter *Comparison of ribosomal RNA (rRNA), begun by

- Often colonial, consisting of small Carl Woese in the 1970s.
aggregations of cells Two very different groups of organisms with
- Some are multicellular prokaryotic cell architecture
- If multicellular, they lack of highly
differentiated tissues a. Bacteria
b. Archaea
Cells exhibited one of two possible “floor plans”
** Protista is not a cohesive taxonomic unit and
a. Prokaryotic cells should be divided into three or more kingdoms. ➔
- Greek pro, before and karyon, nut or kernel; these studies lead to reject the 5-kingdom system in
organisms with a primordial nucleus favor of that divides cellular organisms into three
- Have an open floor plan domains,
- Contents are not divided into
compartments (“rooms”) by 3 Cellular domains
membranes (“walls”)
1. Bacteria (true bacteria or eubacteria)
- Lack the membrane-delimited nucleus
2. Archaea (archaeobacteria, archaebacteria)
observed in Eukaryotic cells
3. Eukarya (all eukaryotic organisms
b. Eukaryotic cells
- Greek eu, true, and karyon, nut or kernel
- Have a nucleus but also many other
membrane-bound organelles
- Separates some cellular materials
and processes from others.
Classification scheme that divided organisms into (5)
five kingdoms
1. Monera
- All organisms with prokaryotic cell structure
2. Protista
3. Fungi
4. Animalia
5. Plantae
*microorganisms (except for viruses and other
acellular infectious agents, which have their own
classification system) were placed in the first three
kingdoms.
Figure 1.2 Universal Phylogenetic Tree. Evolutionary
** the 5-kingsom system is no longer accepted by relationships are based on rRNA sequence
microbiologists comparisons. By Dr. Norman Pace

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 CHAPTER 1: The Evolution of Microorganisms and Microbiology

Bacteria - Many free-living, principal hunters

- Single-celled organisms
- Most have cell walls that contain the
structural molecule peptidoglycan.
- Most exhibit typical prokaryotic cell
structure (lack membrane-bound nucleus)
ex. Phylum Planctomycetes
- Abundant in soil, water, air, extreme
temperatures, pH or salinity
- Major inhabitants of our skin, mouth, and
intestines.
- They contribute to the development of the
body’s immune system.
- Microbes help maintain the health and well-
being of their human hosts.
- Some cause disease:
- The plague (Black death) an
anthropod-borne disease
- Most play beneficial roles:
- Break down dead plant and animal
material
- Make bread, cheese, antibiotics,
vitamins, enzymes and other
products
- Cyanobacteria produce significant amounts
of oxygen.
Archaea
- Distinctive rRNA sequence
- Lack peptidoglycan in their cell wall
- Unique membrane lipids
- Some have unusual metabolic
characteristics, such as the methanogens
which generate methane (natural) gas.
- Found in extreme environments, including
those with high temperatures
(Thermophiles) and high concentrations of
salt (extreme halophiles)
Eukarya
- Microorganisms classified as protists or fungi
- Animals and plants are also placed in this
domain.
1. Protists
- Generally unicellular but larger than most
bacteria and archaea.
Major Protists
a. Algae
- Photosynthetic
- Together with cyanobacteria,
produce about 75% of the plant’s
oxygen
- foundation of aquatic food chains
b. Protozoa
- Unicellular
- Animal-like protists that are motile
and grazers of the microbial world
- Obtain nutrients by ingesting
organic matter
- Found in different environments
and inhabitants of the intestinal
tracts of animals, where they aid in
digestion of complex materials such
as cellulose.
c. Slime molds
- Behave like protozoa in one stage of
their life cycle but like fungi in
another.
- Hunt for and engulf food particles,
consuming decaying vegetation and
other microbes.
d. Water molds
- Protists that grow on the surface of
freshwater and moist soil.
- Feed on decaying vegetation such as
logs and mulch.
- Some produced devasting plant
infections
▪ Ex: Great Potato Famine
2. Fungi
- Range from unicellular forms (yeast) to
molds and mushrooms.
- Moods and mushrooms are multicellular
fungi that form thin, thread-like structure
called Hyphae.
- They absorb nutrients from their
environment, including the organic
molecules the use as sources of
carbon and energy.
- Beneficial roles:
- Bread rise, producing antibiotics and
decomposing dead organisms
- Some fungi associate with plant
roots to form mycorrhizae.
Acellular infectious agents
3. Viruses
- smallest of all microbes
- requires host cell to replicate
- Acellular entities that must invade a host cell
to multiply.
- Composed of proteins and a nucleic acid
- Extremely small
- Smallpox, rabies, influenza, AIDS, common
colds and some cancers.
4. Viroid and satellites
- Composed only of ribonucleic acid (RNA)
Viroid
- Causes numerous plant diseases
Satellites

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 CHAPTER 1: The Evolution of Microorganisms and Microbiology

- Cause plant diseases and some * There must have been a single molecule that could
important animal diseases such as do both cellular work and replicate itself.
hepatitis
5. Prions
- Infectious agents
- Composed of only protein
- Responsible for causing a variety of
spongiform encephalopathies
*Microbes are the dominant organisms on Earth.
Evidence for Origin of Life
Definition of life
- cells and organization
- response to environmental changes
- growth and development
- biological evolution
- energy use and metabolism
- regulation and homeostasis
- reproduction
Attributes of importance to paleobiologist are an:
Thomas Cech, 1981
- Orderly structure
- The ability to obtain and use energy - Discovered a catalytic RNA molecule in a
(metabolism) protist (Tetrahymena sp.)
- Ability to reproduce, *RNA found in ribosomes that is responsible for
Extant organisms forming peptide bonds – bonds that hold together
amino acids, the building blocks of proteins.
- Organisms present today, to explore the
origin of life Ribozymes – catalytic RNA molecules
- Some have the represent “relics” of ancient Original molecule must have fulfilled protein and
life forms hereditary function
Microbial Fossil - Ribozymes
- RNA molecules that form peptide
bonds
* The first discovery of primitive - perform cellular work and
cellular life was the 1977 discovery of replication
microbial fossils in the Swartkoppie - Earliest cells may have been RNA
chert. surrounded by liposomes
Chert is a type of granular Walter Gilbert, 1986
sedimentary rock rich in silica
- Coined the term RNA world
Swartkoppie chert fossils as well as RNA world
those from the Archaean Apex Chart of - To describe a precellular stage in the
Australia have been dated about 3.5 evolution of life in genetic
billion years old. information, as well as catalyzing
Earliest Molecules – RNA other chemical reactions
- A lipid membrane must have formed
Three different molecules fulfill the roles of: around RNA
- Liposomes – vesicle bounded by a lipid
1. Catalysts
bilayer
2. Structural molecules
3. Hereditary molecules Marin Hanczyc, Shelly Fujikawa and Jack Szostak,
2003
Proteins have two major roles in modern cells:
1. Structural
2. Catalytic

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 CHAPTER 1: The Evolution of Microorganisms and Microbiology
- Experiment showed that clay triggers the
formation of liposomes that grow and
divide.
Earliest Molecules – RNA – 2
- Cellular pool of RNA in modern day cells
exists in and is associated with the ribosome
(rRNA, tRNA, mRNA)
- RNA catalytic in protein synthesis
- RNA may be precursor to double
stranded DNA
- Adenosine 5’ triphosphate (ATP) is the
energy currency and is a ribonucleotide
- RNA can regulate gene expression
*Proteins, DNA and cellular energy can be traced
back to RNA
Earliest Metabolism
- Early energy sources under harsh conditions
- inorganics, e.g., FeS
- Photosynthesis
- cyanobacteria evolved 2.5 billion years ago
- Stromatolites – mineralized layers of
microorganisms
The Evolution of metabolism the evolution of
energy-conserving metabolic processes.
Another metabolic strategy, oxygen-releasing
photosynthesis, appears to have evolved as early as
2.5 Billion years ago. ➔ Fossils of cyanobacteria
Evolution of 3 Domains of Life
Dr. Norman Pace
- Developed a universal phylogenetic tree
- Universal phylogenetic tree
- based on comparisons of small
subunit rRNA (SSU rRNA)
- aligned rRNA sequences from
diverse organisms are compared
and differences counted to derive a
value of evolutionary distance
- relatedness, but not time of
divergence, is determined this way.
Last Universal Common Ancestor (LUCA)
- The root or origin of modern life is on
bacterial branch but nature still
controversial
- Archaea and Eukarya evolved independently
of Bacteria
- Archaea and Eukarya diverged from
common ancestry
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Endosymbiotic Hypothesis
- Endosymbiosis is an interaction between
two organisms in which one organism lives
inside the other.
- Origin of three eukaryotic organelles:
1. Mitochondria – bacterial endosymbiont
of an ancestral cell in the eukaryotic
lineage list its ability to live
independently
2. Chloroplasts – if the intracellular
bacterium used aerobic respiration
3. Hydrogenosomes from endosymbiont
- Mitochondria and chloroplasts
- Contain DNA and ribosomes; both
like bacterial DNA and ribosomes
- ISSU rRNA genes show bacterial
lineage
- genome sequences closely related
to bacterium Rickettsia prowazekii
and cyanobacteria genus
Prochloron, respectively
Hydrogenosome
- anaerobic endosymbiont
Hydrogen hypothesis
- endosymbiont was an anaerobic bacterium
that produced H2 and CO2 as end products of
its metabolism.
- The host become dependent of the H2
produced by the endosymbiont.
- The capacity to perform aerobic respiration,
it evolved into a mitochondrion.
Evolution of Cellular Microbes
- Mutation of genetic material led to selected
traits
- New genes and genotypes evolved
- Bacteria and Archaea increase genetic pool
by horizontal gene transfer within the same
generation
Microbial Species
- Eukaryotic microbes fit definition of
reproducing isolated populations
- Bacteria and Archaea do not
reproduce sexually and are referred
to as strains
- a strain consists of descendants of a
single, pure microbial culture
- may be biovars, serovars,
morphovars, pathovars
- binomial nomenclature
- genus and species epithet
 CHAPTER 1: The Evolution of Microorganisms and Microbiology
Microbiology and Its Origins
Roman Philosopher Lucretius (about 98-55 BCE) and
Physician Girolamo Fracastoro (1478 – 1553)
- suggested that disease was caused by
invisible living creatures.
Microbiology – define not only by the organisms it
studies but also by the tools used to study them.
- Microbiologists often remove
microorganisms from their natural habitats
and culture them isolated from other
microbes: this is called Pure or Axenic
culture.
Francesco Stelluti
- Earliest microscopic observation of
organisms
- Using a microscope supplied by Galileo
Robert Hoek
- Credited with publishing the first drawing of
microorganisms in the scientific literature
- Detailed drawing of fungus Mucor in his
book Mircigraphia
- Prototype of the microscopes built
and used by the amateur Antony van
Leeuwenhoek
Antony van Leeuwenhoek of Delft, the Netherlands
- Simple microscope composed double
convex glass lenses held between two silver
plates.
- Magnifies 50 to 300 times
- At 45-degree angle
- Sent detailed letters describing his
discoveries to the Royal Society of London
- Both bacteria and protists
Spontaneous generation – that living organisms
could develop from non-living matter
Who challenged it?
Francesco Redi, Italian Physician
- Discredited spontaneous generation
- showed that maggots on decaying meat
came from fly eggs
John Needham (1713-1781)
- his experiment:
- mutton broth in flasks → boiled
→sealed
- results: broth became cloudy and contained
microorganisms
- he thought organic matter contained a vital
force that could confer the properties of life
on nonliving matter.
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Lazzaro Spallanzani (1729-1799)
- his experiment:
- broth in flasks (water and seeds) →
sealed → boiled
- results: no growth of microorganisms
- he proposed that air carried germs to the
culture medium but also commented that
the external air might be required for growth
of animals already in the medium.
Theodore Schwann
- allowed air to enter flask containing a sterile
nutrient solution after the air had passed
through a red-hot-tube
- results: flask remained sterile
Georg Friedrich Schroder and Theodor von Dusch
- allowed air to enter a flask of heat-sterilized
medium after it had passed through sterile
cotton wool
- results: No growth occurred in the medium
even though the air had not been heated
Pouchet
- claimed in 1959, to have carried out
experiments conclusively proving that
microbial growth could occur without air
contaminations
Louis Pasteur (1822-1895)
- ‘Swan-neck flask’ experiments
- placed nutrient solution in flasks
- created flasks with long, curved
necks
- boiled the solutions
- left flasks exposed to air
- results: no growth of microorganisms
- also showed how to keep solutions sterile
Final Blow to Theory of Spontaneous Generation
John Tyndall (1820-1893)
- demonstrated that dust carries
microorganisms
- showed that if dust was absent, nutrient
broths remained sterile, even if directly
exposed to air
- also provided evidence for the existence of
exceptionally heat-resistant forms of
bacteria
•Ferdinand Cohn (1828-1898)
- heat-resistant bacteria could produce
endospores
 CHAPTER 1: The Evolution of Microorganisms and Microbiology
The Role of Microorganisms in Disease
- Was not immediately obvious
- Infectious disease believed to be due to
supernatural forces or imbalances of 4
bodily-fluid ‘humors’
- Establishing connection depended on
development of techniques for studying
microbes
Greek Physician Galen
- Microorganisms cause diseases – the Germ
Theory of disease.
Agostini Bassi (1773-1856)
- showed that a disease of silkworms was
caused by a fungus
M. J. Berkeley (ca. 1845)
- demonstrated that the great Potato Blight of
Ireland was caused by a water mold
Heinrich de Bary (1853)
- showed that smut and rust fungi caused
cereal crop diseases
Louis Pasteur
- demonstrated microorganisms carried out
fermentations, helping French wine industry
- developed pasteurization to avoid wine
spoilage by microbes
- showed that the pébrine disease of
silkworms was caused by a protozoan
- he did not agree and believed that
fermentations were carried out by living
organisms.
- Pasteurization
Indirect evidence for the germ theory of disease
came from:
Joseph Lister
- provided indirect evidence that
microorganisms were the causal agents of
disease
- developed a system of surgery designed to
prevent microorganisms from entering
wounds as well as methods for treating
instruments and surgical dressings
- his patients had fewer postoperative
infections
- developed a system of antiseptic surgery
designed to prevent microorganisms from
entering wounds
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Robert Koch (1843-1910)
- established the relationship between
Bacillus anthracis and anthrax
- used criteria developed by his teacher Jacob
Henle (1809-1895)
- these criteria now known as Koch’s
postulates
- still used today to establish the link between
a particular microorganism and a particular
disease
Limitations of Koch’s Postulates
- Some organisms cannot be grown in pure
culture
- Using humans in completing the postulates
is unethical
- Molecular and genetic evidence may replace
and overcome these limits
The Development of Techniques for Studying
Microbial Pathogens
Koch’s work led to discovery or development of:
- Agar
- Petri dishes
- nutrient broth and nutrient agar
- methods for isolating microorganisms
Charles Chamberland (1851-1908)
- developed porcelain bacterial filters used by
Ivanoski and Beijerinck to study tobacco
mosaic disease
- determined that extracts from
diseased plants had infectious
agents present which were smaller
than bacteria and passed through
the filters
- infectious agents were eventually
shown to be viruses
Pasteur and Roux
- discovered that incubation of cultures for
long intervals between transfers caused
pathogens to lose their ability to cause
disease (termed ‘attenuation’)
Pasteur and his coworkers
- developed vaccines for chicken cholera,
anthrax, and rabies
Immunological Studies
- once established, led to study of host
defenses - immunology
Edward Jenner (ca. 1798)
- used a vaccination procedure to protect
individuals from smallpox
 CHAPTER 1: The Evolution of Microorganisms and Microbiology

NOTE: this preceded the work establishing the role Major Fields in Microbiology
of microorganisms in disease!
- Medical microbiology – diseases of humans
Emil von Behring (1854-1917) and Shibasaburo and animals
Kitasato (1852-1931) - Public health microbiology – control and
spread of communicable diseases
- developed antitoxins for diphtheria and - Immunology – how the immune system
tetanus protects a host from pathogens
- evidence for humoral (antibody-based) - Microbial ecology is concerned with the
immunity relationship of organisms with their
Elie Metchnikoff (1845-1916) environment
- –less than 1% of earth’s microbial
- discovered bacteria-engulfing, phagocytic population has been cultured
cells in the blood - Agricultural microbiology is concerned with
- evidence for cellular immunity the impact of microorganisms on agriculture
The Development of Industrial Microbiology and - food safety microbiology
Microbial Ecology - animal and plant pathogens
- Industrial microbiology began in the 1800s
Louis Pasteur - fermentation
- antibiotic production
- demonstrated that alcohol fermentations
- production of cheese, bread, etc.
and other fermentations were the result of
- Microbial physiology studies metabolic
microbial activity
pathways of microorganisms
- developed the process of pasteurization to
- Molecular biology, microbial genetics, and
preserve wine during storage
bioinformatics study the nature of genetic
Developments in Microbial Ecology information and how it regulates the
development and function of cells and
Sergei Winogradsky (1856-1953) and Martinus organisms
Beijerinck (1851-1931) - Microbes are a model system of genomics
- studied soil microorganisms and discovered
numerous interesting metabolic processes
(e.g., nitrogen fixation)
- pioneered the use of enrichment cultures
and selective media
Microbiology Has Basic and Applied Aspects
- Basic aspects are concerned with individual
groups of microbes, microbial physiology,
genetics, molecular biology and taxonomy
- Applied aspects are concerned with practical
problems – disease, water, food and
industrial microbiology
Molecular and Genomic Methods
- Led to a second golden age of microbiology
(rapid expansion of knowledge)
Discoveries
- restriction endonucleases (Arber and Smith)
- first novel recombinant molecule (Jackson,
Symons, Berg)
- DNA sequencing methods (Woese, Sanger)
- bioinformatics and genomic sequencing and
analysis

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