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Chapter 1 Evolution of Microorganisms and Micobiology

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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
Microorganisms – organisms and acellular biological
entities too small to be seen clearly by the unaided
eye
-
1 millimeter or less in diameter
Often colonial, consisting of small
aggregations of cells
Some are multicellular
- If multicellular, they lack of highly
differentiated tissues
Cells exhibited one of two possible “floor plans”
a. Prokaryotic cells
- Greek pro, before and karyon, nut or kernel;
organisms with a primordial nucleus
- Have an open floor plan
- Contents are not divided into
compartments
(“rooms”)
by
membranes (“walls”)
- Lack the membrane-delimited nucleus
observed in Eukaryotic cells
(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
(3) Sequences of nucleic acids and protein from
a wide variety of organism have been
compared.
*Comparison of ribosomal RNA (rRNA), begun by
Carl Woese in the 1970s.
Two very different groups of organisms with
prokaryotic cell architecture
a. Bacteria
b. Archaea
** Protista is not a cohesive taxonomic unit and
should be divided into three or more kingdoms. 
these studies lead to reject the 5-kingdom system in
favor of that divides cellular organisms into three
domains,
3 Cellular domains
1. Bacteria (true bacteria or eubacteria)
2. Archaea (archaeobacteria, archaebacteria)
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.
2.
3.
4.
5.
Monera
All organisms with prokaryotic cell structure
Protista
Fungi
Animalia
Plantae
*microorganisms (except for viruses and other
acellular infectious agents, which have their own
classification system) were placed in the first three
kingdoms.
** the 5-kingsom system is no longer accepted by
microbiologists
Roma Flores - 2B1
Figure 1.2 Universal Phylogenetic Tree. Evolutionary
relationships are based on rRNA sequence
comparisons. By Dr. Norman Pace
CHAPTER 1: The Evolution of Microorganisms and Microbiology
Bacteria
-
-
-
-
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 wellbeing 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
-
Many free-living, principal hunters
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
-
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
Roma Flores - 2B1
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
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
5.
-
Cause plant diseases and some
important animal diseases such as
hepatitis
* There must have been a single molecule that could
do both cellular work and replicate itself.
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:
-
Orderly structure
The ability to obtain and use energy
(metabolism)
Ability to reproduce,
Extant organisms
-
Organisms present today, to explore the
origin of life
Some have the represent “relics” of ancient
life forms
Microbial Fossil
* The first discovery of primitive
cellular life was the 1977 discovery of
microbial fossils in the Swartkoppie
chert.
Chert is a type of granular
sedimentary rock rich in silica
Swartkoppie chert fossils as well as
those from the Archaean Apex Chart of
Australia have been dated about 3.5
billion years old.
Thomas Cech, 1981
-
*RNA found in ribosomes that is responsible for
forming peptide bonds – bonds that hold together
amino acids, the building blocks of proteins.
Ribozymes – catalytic RNA molecules
Original molecule must have fulfilled protein and
hereditary function
-
-
-
Three different molecules fulfill the roles of:
Proteins have two major roles in modern cells:
1. Structural
2. Catalytic
Roma Flores - 2B1
Ribozymes
- RNA molecules that form peptide
bonds
- perform
cellular
work
and
replication
Earliest cells may have been RNA
surrounded by liposomes
Walter Gilbert, 1986
Earliest Molecules – RNA
1. Catalysts
2. Structural molecules
3. Hereditary molecules
Discovered a catalytic RNA molecule in a
protist (Tetrahymena sp.)
-
Coined the term RNA world
RNA world
- To describe a precellular stage in the
evolution of life in genetic
information, as well as catalyzing
other chemical reactions
- A lipid membrane must have formed
around RNA
Liposomes – vesicle bounded by a lipid
bilayer
Marin Hanczyc, Shelly Fujikawa and Jack Szostak,
2003
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
Experiment showed that clay triggers the
formation of liposomes that grow and
divide.
Endosymbiotic Hypothesis
-
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.
Hydrogenosome
-
-
-
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.
-
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
Roma Flores - 2B1
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
-
Last Universal Common Ancestor (LUCA)
-
anaerobic endosymbiont
Hydrogen hypothesis
Another metabolic strategy, oxygen-releasing
photosynthesis, appears to have evolved as early as
2.5 Billion years ago.  Fossils of cyanobacteria
-
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
-
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
Lazzaro Spallanzani (1729-1799)
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.
-
Earliest microscopic observation
organisms
Using a microscope supplied by Galileo
of
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.
Roma Flores - 2B1
Theodore Schwann
-
-
Francesco Stelluti
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.
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
endospores
bacteria
could
produce
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
Robert Koch (1843-1910)
-
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)
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
- demonstrated that the great Potato Blight of
Ireland was caused by a water mold
The Development of Techniques for Studying
Microbial Pathogens
Heinrich de Bary (1853)
Koch’s work led to discovery or development of:
-
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
-
Charles Chamberland (1851-1908)
-
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
Agar
Petri dishes
nutrient broth and nutrient agar
methods for isolating microorganisms
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)
-
Roma Flores - 2B1
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
of microorganisms in disease!
Emil von Behring (1854-1917) and Shibasaburo
Kitasato (1852-1931)
-
developed antitoxins for diphtheria and
tetanus
evidence for humoral (antibody-based)
immunity
Major Fields in Microbiology
-
Elie Metchnikoff (1845-1916)
-
discovered bacteria-engulfing, phagocytic
cells in the blood
evidence for cellular immunity
The Development of Industrial Microbiology and
Microbial Ecology
-
-
Louis Pasteur
-
-
demonstrated that alcohol fermentations
and other fermentations were the result of
microbial activity
developed the process of pasteurization to
preserve wine during storage
-
Developments in Microbial Ecology
Sergei Winogradsky (1856-1953) and Martinus
Beijerinck (1851-1931)
-
-
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
Roma Flores - 2B1
Medical microbiology – diseases of humans
and animals
Public health microbiology – control and
spread of communicable diseases
Immunology – how the immune system
protects a host from pathogens
Microbial ecology is concerned with the
relationship of organisms with their
environment
- –less than 1% of earth’s microbial
population has been cultured
Agricultural microbiology is concerned with
the impact of microorganisms on agriculture
- food safety microbiology
- animal and plant pathogens
Industrial microbiology began in the 1800s
- fermentation
- antibiotic production
- production of cheese, bread, etc.
Microbial physiology studies metabolic
pathways of microorganisms
Molecular biology, microbial genetics, and
bioinformatics study the nature of genetic
information and how it regulates the
development and function of cells and
organisms
Microbes are a model system of genomics
R. Stanier and C.B. van Niel
- concept of prokaryote, described
prokaryotes in terms of what they lacked in
comparison to eukaryotic cells.
- Pointed out that prokaryotes lack a
membrane-bound nucleus, a cytoskeleton,
membrane-bound organelles and internal
membranous
structures
such
as
endoplasmic reticulum and Golgi apparatus.
Microorganisms – organisms and acellular biological
entities too small to be seen clearly by the unaided
eye
-
1 millimeter or less in diameter
Often colonial, consisting of small
aggregations of cells
Some are multicellular
- If multicellular, they lack of highly
differentiated tissues
Cells exhibited one of two possible “floor plans”
c. Prokaryotic cells
- Greek pro, before and karyon, nut or kernel;
organisms with a primordial nucleus
- Have an open floor plan
- Contents are not divided into
compartments
(“rooms”)
by
membranes (“walls”)
- Lack the membrane-delimited nucleus
observed in Eukaryotic cells
CHAPTER 1: The Evolution of Microorganisms and Microbiology
Two very different groups of organisms with
prokaryotic cell architecture
c. Bacteria
d. Archaea
** Protista is not a cohesive taxonomic unit and
should be divided into three or more kingdoms. 
these studies lead to reject the 5-kingdom system in
favor of that divides cellular organisms into three
domains,
3 Cellular domains
4. Bacteria (true bacteria or eubacteria)
5. Archaea (archaeobacteria, archaebacteria)
6. Eukarya (all eukaryotic organisms
d. 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
6.
7.
8.
9.
10.
Monera
All organisms with prokaryotic cell structure
Protista
Fungi
Animalia
Plantae
*microorganisms (except for viruses and other
acellular infectious agents, which have their own
classification system) were placed in the first three
kingdoms.
** the 5-kingsom system is no longer accepted by
microbiologists
-
-
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
(4) Learned about the detailed structure of
microbial cells from the use of electron
microscopy.
(5) Microbiologists have determined the
biochemical
and
physiological
characteristics
of
many
different
microorganism
(6) Sequences of nucleic acids and protein from
a wide variety of organism have been
compared.
*Comparison of ribosomal RNA (rRNA), begun by
Carl Woese in the 1970s.
Roma Flores - 2B1
Figure 1.2 Universal Phylogenetic Tree. Evolutionary
relationships are based on rRNA sequence
comparisons. By Dr. Norman Pace
Bacteria
-
-
-
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 wellbeing of their human hosts.
Some cause disease:
- The plague (Black death) an
anthropod-borne disease
Most play beneficial roles:
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
-
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.
6. Protists
- Generally unicellular but larger than most
bacteria and archaea.
Major Protists
e. Algae
- Photosynthetic
- Together
with
cyanobacteria,
produce about 75% of the plant’s
oxygen
- foundation of aquatic food chains
f. Protozoa
- Unicellular
- Animal-like protists that are motile
- Many free-living, principal hunters
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.
g. 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.
h. Water molds
- Protists that grow on the surface of
freshwater and moist soil.
Roma Flores - 2B1
-
Feed on decaying vegetation such as
logs and mulch.
Some produced devasting plant
infections
 Ex: Great Potato Famine
7. 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
8.
-
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.
9. Viroid and satellites
- Composed only of ribonucleic acid (RNA)
Viroid
- Causes numerous plant diseases
Satellites
- Cause plant diseases and some
important animal diseases such as
hepatitis
10. 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
CHAPTER 1: The Evolution of Microorganisms and Microbiology
Attributes of importance to paleobiologist are an:
-
Orderly structure
The ability to obtain and use energy
(metabolism)
Ability to reproduce,
Extant organisms
-
Organisms present today, to explore the
origin of life
Some have the represent “relics” of ancient
life forms
Microbial Fossil
* The first discovery of primitive
cellular life was the 1977 discovery of
microbial fossils in the Swartkoppie
chert.
Chert is a type of granular
sedimentary rock rich in silica
Swartkoppie chert fossils as well as
those from the Archaean Apex Chart of
Australia have been dated about 3.5
billion years old.
Thomas Cech, 1981
-
Discovered a catalytic RNA molecule in a
protist (Tetrahymena sp.)
*RNA found in ribosomes that is responsible for
forming peptide bonds – bonds that hold together
amino acids, the building blocks of proteins.
Earliest Molecules – RNA
Ribozymes – catalytic RNA molecules
Three different molecules fulfill the roles of:
Original molecule must have fulfilled protein and
hereditary function
4. Catalysts
5. Structural molecules
6. Hereditary molecules
-
Proteins have two major roles in modern cells:
3. Structural
4. Catalytic
* There must have been a single molecule that could
do both cellular work and replicate itself.
-
Ribozymes
- RNA molecules that form peptide
bonds
- perform
cellular
work
and
replication
Earliest cells may have been RNA
surrounded by liposomes
Walter Gilbert, 1986
-
-
Coined the term RNA world
RNA world
- To describe a precellular stage in the
evolution of life in genetic
information, as well as catalyzing
other chemical reactions
- A lipid membrane must have formed
around RNA
Liposomes – vesicle bounded by a lipid
bilayer
Marin Hanczyc, Shelly Fujikawa and Jack Szostak,
2003
-
Experiment showed that clay triggers the
formation of liposomes that grow and
divide.
Earliest Molecules – RNA – 2
Roma Flores - 2B1
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
-
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
Endosymbiotic Hypothesis
-
Endosymbiosis is an interaction between
two organisms in which one organism lives
inside the other.
Roma Flores - 2B1
Origin of three eukaryotic organelles:
4. Mitochondria – bacterial endosymbiont
of an ancestral cell in the eukaryotic
lineage list its ability to live
independently
5. Chloroplasts – if the intracellular
bacterium used aerobic respiration
6. 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
Microbiology and Its Origins
Roman Philosopher Lucretius (about 98-55 BCE) and
Physician Girolamo Fracastoro (1478 – 1553)
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
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.
-
Theodore Schwann
-
Francesco Stelluti
-
Earliest microscopic observation
organisms
Using a microscope supplied by Galileo
of
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
-
-
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.
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
-
Antony van Leeuwenhoek of Delft, the Netherlands
-
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.
-
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
endospores
bacteria
could
Lazzaro Spallanzani (1729-1799)
-
his experiment:
Roma Flores - 2B1
The Role of Microorganisms in Disease
produce
CHAPTER 1: The Evolution of Microorganisms and Microbiology
-
-
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)
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
- demonstrated that the great Potato Blight of
Ireland was caused by a water mold
The Development of Techniques for Studying
Microbial Pathogens
Heinrich de Bary (1853)
Koch’s work led to discovery or development of:
-
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
-
Charles Chamberland (1851-1908)
-
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
Agar
Petri dishes
nutrient broth and nutrient agar
methods for isolating microorganisms
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)
Robert Koch (1843-1910)
Roma Flores - 2B1
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
of microorganisms in disease!
Emil von Behring (1854-1917) and Shibasaburo
Kitasato (1852-1931)
-
developed antitoxins for diphtheria and
tetanus
evidence for humoral (antibody-based)
immunity
Major Fields in Microbiology
-
Elie Metchnikoff (1845-1916)
-
discovered bacteria-engulfing, phagocytic
cells in the blood
evidence for cellular immunity
The Development of Industrial Microbiology and
Microbial Ecology
-
-
Louis Pasteur
-
-
demonstrated that alcohol fermentations
and other fermentations were the result of
microbial activity
developed the process of pasteurization to
preserve wine during storage
-
Developments in Microbial Ecology
Sergei Winogradsky (1856-1953) and Martinus
Beijerinck (1851-1931)
-
-
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
Roma Flores - 2B1
-
-
Medical microbiology – diseases of humans
and animals
Public health microbiology – control and
spread of communicable diseases
Immunology – how the immune system
protects a host from pathogens
Microbial ecology is concerned with the
relationship of organisms with their
environment
- –less than 1% of earth’s microbial
population has been cultured
Agricultural microbiology is concerned with
the impact of microorganisms on agriculture
- food safety microbiology
- animal and plant pathogens
Industrial microbiology began in the 1800s
- fermentation
- antibiotic production
- production of cheese, bread, etc.
Microbial physiology studies metabolic
pathways of microorganisms
Molecular biology, microbial genetics, and
bioinformatics study the nature of genetic
information and how it regulates the
development and function of cells and
organisms
Microbes are a model system of genomics
R. Stanier and C.B. van Niel
- concept of prokaryote, described
prokaryotes in terms of what they lacked in
comparison to eukaryotic cells.
- Pointed out that prokaryotes lack a
membrane-bound nucleus, a cytoskeleton,
membrane-bound organelles and internal
membranous
structures
such
as
endoplasmic reticulum and Golgi apparatus.
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