Lecture 1

1) Which of the following attributes make some microorganisms ideal model

systems for studying life's basic processes?
A
They have low mutation rates
B
They grow to high cell densities in a short amount of time
C
Their limited diversity allowed thorough characterization of basic processes
D
Most microorganisms cause disease and are at the centre of human
activity.
Microorganisms have a high mutation rate (much higher than we have), but this
is not a good reason for studying them.
Most microorganisms are very beneficial, we are dependent on them. Only a few
are bad.
2) What is the name of the process in which cells take up nutrients from the
environment and convert them into new cell structures and waste products?
A
differentiation
B
evolution
C
cell signalling
D
metabolism
3) What is the immediate environment called where a microbial population lives?
A
ecosystem
B
biome
C
landscape
D
habitat
4) Of the following evolutionary milestones, which occurred earlier than
oxygenation of Earth's atmosphere?
A
appearance of eukaryotes
B
origin of cyanobacteria
C
development of algal diversity
D
appearance of shelled invertebrates
Oxygenic photosynthesis must have occurred before so that oxygen could rise in
our atmospheres.
Shelled invertebrates are eukaryotes; algae are eukaryotes and eukaryotes all
came after the oxygenation of the Earth's atmosphere.
5) What are the crop plants called that form symbiotic relations with the bacteria
that convert nitrogen gas into ammonia?
A
fruits
B
legumes
C
grains
D
dicotyls
legumes = vlinderbloemen.

6) What is the method called that uses selective culture media and incubation
conditions to isolate specific microorganisms from natural samples?
A
dilution culture
B
anaerobic culture
C
enrichment culture
D
streaking
7) Consider the following two statements:
I Most bacterial species cause diseases.
II Infectious diseases are the leading cause of death in the United States today.
Answer: Neither statement I nor II are correct.
Microbiology contributed to the improvement of human health in the last century
by:
inventing safe drinking water
cleaning wastewater
discovering antibiotics
vaccination programmes
A Winogradsky column: mimicking a freshwater lake.
There is an enormous diversity in microorganisms.
Eukaryotes depend on microorganisms: rumen system/nitrogen fixing nodules.
Practical - good to know

Lecture 2
Microbiology = science that revolves around two important aspects:
1) understanding basic life processes
microbes are excellent models for understanding cellular processes in
unicellular as well as multicellular organisms.
2) applying that knowledge to the benefit of humans
microbes play important roles in medicine, agriculture, and industry.
Microorganisms grow very fast, there are many of them, they are genetically
accessible: many aspects that can help us understand the basic aspects of life.
5 important reasons why microorganisms are important/important to study them
oldest form of life (~4 billion years)
largest mass of living material on Earth (50% of biomass on earth =
microbes. 49% = plants and 1% animals that contribute to the biomass on
earth.)

Carry out major processes for biogeochemical cycles.

All biogeochemical cycles depend on microorganisms; the nitrogen cycle,
carbon cycle, phosphor cycle and all mineralization processes depend on
microorganisms.
can live in places unsuitable for other organisms.
can inhabit every place on earth.
other life forms require microbes to survive
Plants cannot live without microorganisms, animals depend on intimate
symbiosis with microorganisms.

We are a microbial planet.

Microoganisms: are with very many, they are small and you need a microscope to
see them.
They are on this planet for about 4 billion years (plants: 450 million years ago
that the first plants arose).
For at least the first 2 billion years: life on planet exclusively anaerobic. And still
many microbes do not need oxygen to live (we do).
7 processes where microorganisms are important:
1. nitrogen (stikstof)
microorganisms fix nitrogen for plants. they provide nitrogen for our
growth.
NITROGEN FIXATION AND CROP PROTECTION
2. oxygen.
plants make oxygen, but half of the oxygen is made by cyanobacteria in
the ocean.
HEALTHY AIR AND OXYGEN
3. Wastewater.
microbes help us to make wastewater clean again.
CLEAN ENVIRONMENT AND WASTEWATER.
4. Gas
production of greenhouse gases: carbon dioxide, methane nitrous oxide.
GHG PRODUCTION AND MITIGATION
5. Human microbiome
6. Source of new medicines and bioproducts
It is possible to live without microbes.
CLD: centrum voor proefdieren.
There they have animals and plants without microorganisms. These are called
gnotobiotic (without microorganisms)
Why would the mice need microorganisms: for digestion.
they need to be fed sterile food. It needs vitamins, carbohydrates, fats proteins.
The food needs to be grinded well.
gnotobiotic mice have:
lesser bowel movement
reduced immune system - has never been challenged since they live in a bubble
reduced organs
severe nutritional requirements

from birth, we have been and are constantly being challenged with
microorganisms around us. We get used to it, as we progress into adulthood our
immune system gets better.
If the mouse would be taken out of the bubble, it most likely could not even
survive for a day because of the sudden exposure to pathogens.
Microbes are very important on this earth
without microbes, no life
element cycles
degradation of organic matter
O2 production
very many beneficial microbes, very few pathogens
enormous metabolic potential
50% of biomass on earth
reservoir of nitrogen and phosphor

Difference between prokaryotic and eukaryotic cells.

a yeast is a eukaryote.
light microscope is good to see plant and animal cells, these are 100-200
micrometers big.
Normally a bacterial cell is only 1 micrometer; barely visible with a light
microscope so you often use an electron microscope with much better
magnification and resolution.

So standard basic function of the cell are on the chromosome, special functions
are encoded on plasmids.
E. coli has about 4300 genes.
the human has 7 times more genes than E. coli. We have more DNA, but a lot is
non-coding.
Metabolism: take up of nutrients -> conversion of nutrients -> waste products
each bacterial cell needs to become 2 cells if they want to grow -> reproduction

prokaryotes allow small rate of mutation -> if beneficial; it is retained in the

genetic material.
If the mutation is not beneficial, the cells will die and in this way the population
evolves into the fittest species.
some prokaryotes can do differentiation (spore forming to survive harsh
condition)
Communication by exchanging DNA but also by chemicals.
Bacterial cells communicate via chemicals.
they excrete certain chemicals which can be sensed by other cells, these cells on
their turn get triggered by this.
If a cell excretes an antibiotic, other cells will sense this antibiotic, they either
take it up and die or swim away.
exchange of genetic information and bacterial cells can use flagella to swim; they
are motile.
For metabolism, you need the information to encode the metabolism on the
genes.
the genes need to be transcribed from DNA -> RNA . RNA needs to be translated
into protein at the ribosomes.

the first self-replication entities may not have been cells.

LUCA = last universal common ancestor (LUCA): common ancestral cell from
which all cells descended.

by isotope carbon dating we believe the earth is about 4.5 billion years old.
first microbial cells appeared about 4 billion years ago.
when there was enough oxygen, eukaryotes could rise.

phylogenetic tree; family tree of microorganisms. 16srRNA molecule to determine

the relationship between different microorganisms.
sample -> extract DNA -> make more DNA polymerase chain reaction (for which
enzyme DNA polymerase is needed; this needs to withstand high temperatures),
primers complementary to the 16srRNA; one for-primer and one back primer. PCR
AMPLIFICATION.
analyze sequence information -> generate phylogenetic tree depiction
relationships of different microorganisms.

endosymbiosis theory
event where a hydrogen producing bacteria were engulfed by hydrogen
consuming archae -> gave rise to eukaryotes.

Microorganisms seldomly live alone, they always live in populations

the environment in which a microbial population lives is a habitat

individual cell = exception

population = cells in association. microbial cells live in a population, clonal
populations of 1 cell.
community = several populations together.
habitat = place where community lives
ecosystem = microorganisms and their physicochemical environment.
microbes can live in conditions we can't.
they can life in ice and in hot springs
they can life in different in acid lakes
can withstand salt, oxygen and pressure.