Foundations I
Introduction:
Microbiology = the biology of microorganisms. That is a single cell, a cluster of cells or a
virus. We use microbiology for 2 general themes: understanding nature of life and deal with
problems in medicine, agriculture and industry.
Microbes are the oldest form of life. They are the largest mass of living material on earth.
They carry out major processes for biogeochemical cycles. Other lives rely on the microbes.
Most microbes are single celled organism but can form a complex with multiple microbes.
Pure culture is used in the lab (petri plates), a single colony are about 10^7 individual cells.
The cell is a dynamic entity that forms the fundamental unit of life. There are prokaryotes
and eukaryotes. The major differences are:
prokaryotes eukaryotes
- nu nucleus but a nucleoid - cells are generally larger
- often smaller than eukaryotes - often more complex than proka.
- often contain plasmids - often contain various organelles
- no membrane-enclosed organelles - DNA enclosed in a membrane
bound nucleus
Properties of microbial cells:
metabolism: genetic (translation, replication) & catalytic (energy)
growth: nutrients from the environment are converted into cell material
evolution: cells evolve to display new properties.
Properties of some microbial cells:
differentiation: form new structures such as pores
communication: interact via chemical messengers
genetic exchange: exchange genes
motility: some cells are capable of moving, via flagellum for example
Microbial ecology: a microbial habitat is the location in where a microbial population lives.
They can interact with the physical and chemical environment. That interaction can be
harmful but also beneficial. The diversity and abundances are controlled by resources
(nutrients) and environmental conditions (temperature, pH, O2)
Microbial cells are in total of the whole world around 2 x 10^30 cells.
The impact of microorganisms on humans:
Microorganism can have positive (energy, agriculture) and negative effects (disease,
spoilage). Now days we know a lot more about microorganism and less people die because
of them.
We life in symbioses with microbes:
The number of microbial cells in our body is 10^13-10^14. We use them in modern
agriculture (N-cycle = koolsofkringloop) and they create nutrients and waist products.
The gut microbiome is a major contribute to human health. And we use them in our food,
from glucose, to prevent spoilage by fermentation products. Also, glucose can become
ethanol via fermentation, so it is a biofuel.
They are also used to clean up wastes: organic pollutants, wastewater & spilled oil.
, Lessons from history:
Pasteur: spontaneous mutations. If you heat something, there will be no growth. If you make
contact with the liquid and the microorganism, they will go together. This work is important
for the idea of sterilization. So, they don’t merge spontaneously form non-living.
Koch: a set of four postulates, to prove that a specific microorganism can causes specific
diseases. He tried it with an animal and the disease, to later isolate the animal. But there
were limitations to this: not all diseases and animals and humans are the same, many
bacteria do not grow in pure cultures on plates and viruses cannot be grown on plates.
Beijerinck: he developed the enrichment culture technique. Specific microorganisms have
specific culture media and conditions. Later on, he discovered also viruses.
The unity and diversity of life:
We can study applied microbiology: in medical, agriculture, aquatic and industrial.
We also can study the basics: systematics, ecology, genetics, physiology, biochemistry.
Cracking the code of life:
Griffith that discovered transformation of R into S, Avery-MacLeod-McCarthy discovered that
R into S by transfer of DNA and Watson-Crick are the double helix DNA and the 4 bases in
every organism.
Woese and the tree of life:
Via evolution, process of change over time results in new varieties and species of organism.
Phylogeny = the evolutionary relationship between organisms. This relationship can be
deduced by comparing genetic information in the specimens. The use of ribosomal RNA
(rRNA) is an excellent way to determine this because: universal, functionally constant, highly
conserved and of adequate length.
Via this way, we defined three district
lineages of cell domains: bacteria
(prokaryotic), archaea (prokaryotic) and
eukaryote (eukaryotic).
Archaea and bacteria are not closely related,
archaea and eukaryote are more related.
This is built via a cultivation-dependent
r method. So, everything in the scheme can
be seen in the lab.
R
N
If we A take samples from a cultivation-
independent method, we can
add so much more bacteria domains
because a lot of them don’t grow in the lab.
Viruses are not included into the tree of life,
because they lac ribosomal RNA.
Introduction:
Microbiology = the biology of microorganisms. That is a single cell, a cluster of cells or a
virus. We use microbiology for 2 general themes: understanding nature of life and deal with
problems in medicine, agriculture and industry.
Microbes are the oldest form of life. They are the largest mass of living material on earth.
They carry out major processes for biogeochemical cycles. Other lives rely on the microbes.
Most microbes are single celled organism but can form a complex with multiple microbes.
Pure culture is used in the lab (petri plates), a single colony are about 10^7 individual cells.
The cell is a dynamic entity that forms the fundamental unit of life. There are prokaryotes
and eukaryotes. The major differences are:
prokaryotes eukaryotes
- nu nucleus but a nucleoid - cells are generally larger
- often smaller than eukaryotes - often more complex than proka.
- often contain plasmids - often contain various organelles
- no membrane-enclosed organelles - DNA enclosed in a membrane
bound nucleus
Properties of microbial cells:
metabolism: genetic (translation, replication) & catalytic (energy)
growth: nutrients from the environment are converted into cell material
evolution: cells evolve to display new properties.
Properties of some microbial cells:
differentiation: form new structures such as pores
communication: interact via chemical messengers
genetic exchange: exchange genes
motility: some cells are capable of moving, via flagellum for example
Microbial ecology: a microbial habitat is the location in where a microbial population lives.
They can interact with the physical and chemical environment. That interaction can be
harmful but also beneficial. The diversity and abundances are controlled by resources
(nutrients) and environmental conditions (temperature, pH, O2)
Microbial cells are in total of the whole world around 2 x 10^30 cells.
The impact of microorganisms on humans:
Microorganism can have positive (energy, agriculture) and negative effects (disease,
spoilage). Now days we know a lot more about microorganism and less people die because
of them.
We life in symbioses with microbes:
The number of microbial cells in our body is 10^13-10^14. We use them in modern
agriculture (N-cycle = koolsofkringloop) and they create nutrients and waist products.
The gut microbiome is a major contribute to human health. And we use them in our food,
from glucose, to prevent spoilage by fermentation products. Also, glucose can become
ethanol via fermentation, so it is a biofuel.
They are also used to clean up wastes: organic pollutants, wastewater & spilled oil.
, Lessons from history:
Pasteur: spontaneous mutations. If you heat something, there will be no growth. If you make
contact with the liquid and the microorganism, they will go together. This work is important
for the idea of sterilization. So, they don’t merge spontaneously form non-living.
Koch: a set of four postulates, to prove that a specific microorganism can causes specific
diseases. He tried it with an animal and the disease, to later isolate the animal. But there
were limitations to this: not all diseases and animals and humans are the same, many
bacteria do not grow in pure cultures on plates and viruses cannot be grown on plates.
Beijerinck: he developed the enrichment culture technique. Specific microorganisms have
specific culture media and conditions. Later on, he discovered also viruses.
The unity and diversity of life:
We can study applied microbiology: in medical, agriculture, aquatic and industrial.
We also can study the basics: systematics, ecology, genetics, physiology, biochemistry.
Cracking the code of life:
Griffith that discovered transformation of R into S, Avery-MacLeod-McCarthy discovered that
R into S by transfer of DNA and Watson-Crick are the double helix DNA and the 4 bases in
every organism.
Woese and the tree of life:
Via evolution, process of change over time results in new varieties and species of organism.
Phylogeny = the evolutionary relationship between organisms. This relationship can be
deduced by comparing genetic information in the specimens. The use of ribosomal RNA
(rRNA) is an excellent way to determine this because: universal, functionally constant, highly
conserved and of adequate length.
Via this way, we defined three district
lineages of cell domains: bacteria
(prokaryotic), archaea (prokaryotic) and
eukaryote (eukaryotic).
Archaea and bacteria are not closely related,
archaea and eukaryote are more related.
This is built via a cultivation-dependent
r method. So, everything in the scheme can
be seen in the lab.
R
N
If we A take samples from a cultivation-
independent method, we can
add so much more bacteria domains
because a lot of them don’t grow in the lab.
Viruses are not included into the tree of life,
because they lac ribosomal RNA.
