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- 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
- Earliest microscopic observation of Georg Friedrich Schroder and Theodor von Dusch
organisms - allowed air to enter a flask of heat-sterilized
- Using a microscope supplied by Galileo medium after it had passed through sterile
Robert Hoek cotton wool
- results: No growth occurred in the medium
- Credited with publishing the first drawing of even though the air had not been heated
microorganisms in the scientific literature
- Detailed drawing of fungus Mucor in his Pouchet
book Mircigraphia - claimed in 1959, to have carried out
- Prototype of the microscopes built experiments conclusively proving that
and used by the amateur Antony van microbial growth could occur without air
Leeuwenhoek contaminations
Antony van Leeuwenhoek of Delft, the Netherlands Louis Pasteur (1822-1895)
- Simple microscope composed double - ‘Swan-neck flask’ experiments
convex glass lenses held between two silver - placed nutrient solution in flasks
plates. - created flasks with long, curved
- Magnifies 50 to 300 times necks
- At 45-degree angle - boiled the solutions
- Sent detailed letters describing his - left flasks exposed to air
discoveries to the Royal Society of London - results: no growth of microorganisms
- Both bacteria and protists - also showed how to keep solutions sterile
Spontaneous generation – that living organisms Final Blow to Theory of Spontaneous Generation
could develop from non-living matter
John Tyndall (1820-1893)
Who challenged it?
- demonstrated that dust carries
Francesco Redi, Italian Physician microorganisms
- Discredited spontaneous generation - showed that if dust was absent, nutrient
- showed that maggots on decaying meat broths remained sterile, even if directly
came from fly eggs exposed to air
- also provided evidence for the existence of
John Needham (1713-1781) exceptionally heat-resistant forms of
- his experiment: bacteria
- mutton broth in flasks boiled •Ferdinand Cohn (1828-1898)
sealed
- results: broth became cloudy and contained - heat-resistant bacteria could produce
microorganisms endospores
- he thought organic matter contained a vital
force that could confer the properties of life
on nonliving matter.
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 - R. Stanier and C.B. van Niel
numerous interesting metabolic processes - - concept of prokaryote, described
(e.g., nitrogen fixation) prokaryotes in terms of what they lacked in
- pioneered the use of enrichment cultures comparison to eukaryotic cells.
and selective media - - Pointed out that prokaryotes lack a
membrane-bound nucleus, a cytoskeleton,
Microbiology Has Basic and Applied Aspects membrane-bound organelles and internal
membranous structures such as
- Basic aspects are concerned with individual
endoplasmic reticulum and Golgi apparatus.
groups of microbes, microbial physiology,
genetics, molecular biology and taxonomy Microorganisms – organisms and acellular biological
- Applied aspects are concerned with practical entities too small to be seen clearly by the unaided
problems – disease, water, food and eye
industrial microbiology
- 1 millimeter or less in diameter
Molecular and Genomic Methods - Often colonial, consisting of small
aggregations of cells
- Led to a second golden age of microbiology
- Some are multicellular
(rapid expansion of knowledge)
- If multicellular, they lack of highly
Discoveries differentiated tissues
- restriction endonucleases (Arber and Smith) Cells exhibited one of two possible “floor plans”
- first novel recombinant molecule (Jackson,
c. Prokaryotic cells
Symons, Berg)
- Greek pro, before and karyon, nut or kernel;
- DNA sequencing methods (Woese, Sanger)
organisms with a primordial nucleus
- bioinformatics and genomic sequencing and
- Have an open floor plan
analysis
- Contents are not divided into
compartments (“rooms”) by
membranes (“walls”)
- Lack the membrane-delimited nucleus
observed in Eukaryotic cells
- Break down dead plant and animal - Feed on decaying vegetation such as
material logs and mulch.
- Make bread, cheese, antibiotics, - Some produced devasting plant
vitamins, enzymes and other infections
products Ex: Great Potato Famine
- Cyanobacteria produce significant amounts 7. Fungi
of oxygen. - Range from unicellular forms (yeast) to
molds and mushrooms.
Archaea - Moods and mushrooms are multicellular
- Distinctive rRNA sequence fungi that form thin, thread-like structure
- Lack peptidoglycan in their cell wall called Hyphae.
- Unique membrane lipids - They absorb nutrients from their
- Some have unusual metabolic environment, including the organic
characteristics, such as the methanogens molecules the use as sources of
which generate methane (natural) gas. carbon and energy.
- Found in extreme environments, including - Beneficial roles:
those with high temperatures - Bread rise, producing antibiotics and
(Thermophiles) and high concentrations of decomposing dead organisms
salt (extreme halophiles) - Some fungi associate with plant
roots to form mycorrhizae.
Eukarya
Acellular infectious agents
- Microorganisms classified as protists or fungi
- Animals and plants are also placed in this 8. Viruses
domain. - smallest of all microbes
6. Protists - requires host cell to replicate
- Generally unicellular but larger than most - Acellular entities that must invade a host cell
bacteria and archaea. to multiply.
- Composed of proteins and a nucleic acid
Major Protists - Extremely small
e. Algae - Smallpox, rabies, influenza, AIDS, common
- Photosynthetic colds and some cancers.
- Together with cyanobacteria,
produce about 75% of the plant’s 9. Viroid and satellites
oxygen - Composed only of ribonucleic acid (RNA)
- foundation of aquatic food chains Viroid
f. Protozoa - Causes numerous plant diseases
- Unicellular Satellites
- Animal-like protists that are motile - Cause plant diseases and some
- Many free-living, principal hunters important animal diseases such as
and grazers of the microbial world hepatitis
- Obtain nutrients by ingesting 10. Prions
organic matter - Infectious agents
- Found in different environments - Composed of only protein
and inhabitants of the intestinal - Responsible for causing a variety of
tracts of animals, where they aid in spongiform encephalopathies
digestion of complex materials such *Microbes are the dominant organisms on Earth.
as cellulose.
g. Slime molds Evidence for Origin of Life
- Behave like protozoa in one stage of
their life cycle but like fungi in Definition of life
another. - cells and organization
- Hunt for and engulf food particles, - response to environmental changes
consuming decaying vegetation and - growth and development
other microbes. - biological evolution
h. Water molds - energy use and metabolism
- Protists that grow on the surface of - regulation and homeostasis
freshwater and moist soil. - reproduction
Three different molecules fulfill the roles of: Original molecule must have fulfilled protein and
hereditary function
4. Catalysts
5. Structural molecules - Ribozymes
6. Hereditary molecules - RNA molecules that form peptide
bonds
Proteins have two major roles in modern cells: - perform cellular work and
replication
3. Structural
- Earliest cells may have been RNA
4. Catalytic surrounded by liposomes
* There must have been a single molecule that could
Walter Gilbert, 1986
do both cellular work and replicate itself.
- 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
- Cellular pool of RNA in modern day cells - Origin of three eukaryotic organelles:
exists in and is associated with the ribosome 4. Mitochondria – bacterial endosymbiont
(rRNA, tRNA, mRNA) of an ancestral cell in the eukaryotic
- RNA catalytic in protein synthesis lineage list its ability to live
- RNA may be precursor to double independently
stranded DNA 5. Chloroplasts – if the intracellular
- Adenosine 5’ triphosphate (ATP) is the bacterium used aerobic respiration
energy currency and is a ribonucleotide 6. Hydrogenosomes from endosymbiont
- RNA can regulate gene expression - Mitochondria and chloroplasts
- Contain DNA and ribosomes; both
*Proteins, DNA and cellular energy can be traced like bacterial DNA and ribosomes
back to RNA - ISSU rRNA genes show bacterial
Earliest Metabolism lineage
- genome sequences closely related
- Early energy sources under harsh conditions to bacterium Rickettsia prowazekii
- inorganics, e.g., FeS and cyanobacteria genus
- Photosynthesis Prochloron, respectively
- cyanobacteria evolved 2.5 billion years ago
- Stromatolites – mineralized layers of Hydrogenosome
microorganisms - anaerobic endosymbiont
The Evolution of metabolism the evolution of Hydrogen hypothesis
energy-conserving metabolic processes.
- endosymbiont was an anaerobic bacterium
Another metabolic strategy, oxygen-releasing that produced H2 and CO2 as end products of
photosynthesis, appears to have evolved as early as its metabolism.
2.5 Billion years ago. Fossils of cyanobacteria - The host become dependent of the H2
Evolution of 3 Domains of Life produced by the endosymbiont.
- The capacity to perform aerobic respiration,
Dr. Norman Pace it evolved into a mitochondrion.
- Developed a universal phylogenetic tree Evolution of Cellular Microbes
- Universal phylogenetic tree
- based on comparisons of small - Mutation of genetic material led to selected
subunit rRNA (SSU rRNA) traits
- aligned rRNA sequences from - New genes and genotypes evolved
diverse organisms are compared - Bacteria and Archaea increase genetic pool
and differences counted to derive a by horizontal gene transfer within the same
value of evolutionary distance generation
- relatedness, but not time of Microbial Species
divergence, is determined this way.
- Eukaryotic microbes fit definition of
Last Universal Common Ancestor (LUCA)
reproducing isolated populations
- The root or origin of modern life is on - Bacteria and Archaea do not
bacterial branch but nature still reproduce sexually and are referred
controversial to as strains
- Archaea and Eukarya evolved independently - a strain consists of descendants of a
of Bacteria single, pure microbial culture
- Archaea and Eukarya diverged from - may be biovars, serovars,
common ancestry morphovars, pathovars
- binomial nomenclature
- genus and species epithet
- suggested that disease was caused by - broth in flasks (water and seeds)
invisible living creatures. sealed boiled
- results: no growth of microorganisms
Microbiology – define not only by the organisms it
- he proposed that air carried germs to the
studies but also by the tools used to study them. culture medium but also commented that
- Microbiologists often remove the external air might be required for growth
microorganisms from their natural habitats of animals already in the medium.
and culture them isolated from other Theodore Schwann
microbes: this is called Pure or Axenic
culture. - allowed air to enter flask containing a sterile
nutrient solution after the air had passed
Francesco Stelluti through a red-hot-tube
- Earliest microscopic observation of - results: flask remained sterile
organisms Georg Friedrich Schroder and Theodor von Dusch
- Using a microscope supplied by Galileo
- allowed air to enter a flask of heat-sterilized
Robert Hoek medium after it had passed through sterile
- Credited with publishing the first drawing of cotton wool
microorganisms in the scientific literature - results: No growth occurred in the medium
- Detailed drawing of fungus Mucor in his even though the air had not been heated
book Mircigraphia Pouchet
- Prototype of the microscopes built
and used by the amateur Antony van - claimed in 1959, to have carried out
Leeuwenhoek experiments conclusively proving that
microbial growth could occur without air
Antony van Leeuwenhoek of Delft, the Netherlands contaminations
- Simple microscope composed double Louis Pasteur (1822-1895)
convex glass lenses held between two silver
plates. - ‘Swan-neck flask’ experiments
- Magnifies 50 to 300 times - placed nutrient solution in flasks
- At 45-degree angle - created flasks with long, curved
- Sent detailed letters describing his necks
discoveries to the Royal Society of London - boiled the solutions
- Both bacteria and protists - left flasks exposed to air
- results: no growth of microorganisms
Spontaneous generation – that living organisms - also showed how to keep solutions sterile
could develop from non-living matter
Final Blow to Theory of Spontaneous Generation
Who challenged it?
John Tyndall (1820-1893)
Francesco Redi, Italian Physician
- demonstrated that dust carries
- Discredited spontaneous generation microorganisms
- showed that maggots on decaying meat - showed that if dust was absent, nutrient
came from fly eggs broths remained sterile, even if directly
John Needham (1713-1781) exposed to air
- also provided evidence for the existence of
- his experiment: exceptionally heat-resistant forms of
- mutton broth in flasks boiled bacteria
sealed
- results: broth became cloudy and contained •Ferdinand Cohn (1828-1898)
microorganisms - heat-resistant bacteria could produce
- he thought organic matter contained a vital endospores
force that could confer the properties of life
on nonliving matter.
Lazzaro Spallanzani (1729-1799)
- his experiment: The Role of Microorganisms in Disease
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 - R. Stanier and C.B. van Niel
numerous interesting metabolic processes - - concept of prokaryote, described
(e.g., nitrogen fixation) prokaryotes in terms of what they lacked in
- pioneered the use of enrichment cultures comparison to eukaryotic cells.
and selective media - - Pointed out that prokaryotes lack a
membrane-bound nucleus, a cytoskeleton,
Microbiology Has Basic and Applied Aspects membrane-bound organelles and internal
membranous structures such as
- Basic aspects are concerned with individual
endoplasmic reticulum and Golgi apparatus.
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