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Summary microbiology (microbiology&biochemistry) wur
- Instelling
- Wageningen University (WUR)
A summary of microbiology for the course Microbiology and Biochemistry.
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Biology of microorganismssummary
By Emma Burgwal, wur
Chapter 1
1.1 Microorganisms are forms of life too small to be seen by the human eye. They are diverse in
form and function and typically live together in complex microbial communities. Microbiology is
all about microorganisms and the effect they have on our planet. They represent a major fraction
of Earth’s biomass and their activities are essential for life.
Researchers can investigate microorganisms with a microscope. A culture is a collection of cells
grown in a neutral medium. A medium is a nutrient mixture. Growth is the increase in cell
number. Cells can grow in a colony. Microorganisms can rapidly grow under controlled
conditions.
1.2 All cells have a permeability barrier called the cytoplasmatic membrane. It separates the
cytoplasm from the outside. This is a mixture of macromolecules, small organic molecules,
inorganic ions and ribosomes. Ribosomes are responsible for protein synthesis. Some cells
(plants) have a cell wall that lends structural strength.
You have prokaryotic (without nucleus) and eukaryotic (with nucleus) cells. Eukaryotic cells have
organelles, such as mitochondria.
All cells possess a genome; a complement of all genes in a cell. A gene is a segment of DNA. In
eukaryotes, thins genome lays in a nucleus. Prokaryotes have circular DNA in the cytoplasm. This
forms the nucleoid. They can also have plasmids, which contain genes that are not essential but
confer special functions.
Cells show metabolism; taking nutrients and converting them in new cell materials or waste
products. Enzymes regulate these processes. Transcription copies DNA in RNA and translation
translates RNA to a protein or enzyme. Microbial growth consists of DNA replication followed by
division.
Some cells are capable of motility, some undergo differentiation. Cells have intercellular
communication and most can exchange genes with neighbouring cells (horizontal gene transfer).
Evolution is when genes change over time, leading to modification.
1.3 Microorganisms appeared between 3.8 and 4.3 billion years ago. At first, Earth (4.6 billion years
old) was anoxic (for 2 billion of years). After 1 billion years: phototropic microorganisms
occurred. They were anaerobic at first. Cyanobacteria (1 billion years later) began with oxidizing.
After that, all multicellular forms of life formed.
There are three major cell lineages; bacteria, archaea and eukaryotes. These are called domains.
All these domains have a common ancestor (LUCA) (science of microbial ecology).
Estimated is that there more microorganisms then stars. Microorganisms can occur in extreme
conditions, like lava. These types of microorganisms are called extremophiles.
The metabolic activity of microorganisms can change our habitat.
1.4 The major causes of human death were because of bacterial and viral pathogens (beginning
twentieth century). But, most microorganisms are not harmful but useful for humans. Agriculture
benefits from nodules, who convert nitrogen to ammonia (=nitrogen fixation).
, Food growth has also been influenced by microorganisms. Some are harmful, other very useful
(for example in cheese). They also have an impact on the industry, such as antibiotics,
wastewater or biofuels.
1.5 Robert Hooke wrote the first known description of microorganisms. Antoni van Leeuwenhoek
was the first person to see bacteria. His microscope was a light microscope, with visible light. The
principle of magnification, enlarging an image, played an important role. The limiting factor with
this type of microscope is resolution, the ability to distinguish objects.
Nowadays, several types of light microscopes are available. Specimens are visible because of
difference in contrast.
The limit of resolution is defined by the wavelength of light and the light-gathering ability of the
lens (numerical aperture).
1.6 Staining: dyes improve contrast. Used for bright-field microscopy. It is common to observe dried
preparations of cells.
Gram stain: stains that render different kinds of cells different colours. With the Gram-stain,
bacteria can be divided in gram-positive and gram-negative.
Phase-contrast: staining often kills cells. This principle differs cells in refractive index. A phase
ring can change this refractive index.
Dark-field microscopy: the specimen appears light on a dark background.
Fluorescence microscopy: cells are made to fluorescence, for example with DAPI.
1.7 Differential interference contrast microscopy (DIC) contains a polarizer in the condenser to
produce polarized light. This passes through a prism. This provides a three-dimensional image. A
confocal scanning laser microscope (CSLM) is computer-controlled. It couples a laser to
fluorescent. Only one layer of the cell is at perfect focus. The computer makes a 3D image of
these layers.
1.8 Electron microscopes use electrons instead of light. Electromagnets functions as lenses. They
have a camera to take photographs, electron micrographs.
Transmission electron microscope (TEM): examines cell structure. The wavelength of electrons is
shorter than of light, so the resolution is higher. Staining with chemicals also makes structure
visible with the TEM. With negative staining can intact cells be observed.
Scanning electron microscope (SEM): for 3D images. The specimen is coated with a thin film of
heavy metal.
Images of both are black and white. Colour is often added by manipulating in the computer.
1.9 Pasteur studied the formation of crystals during production of alcohol. He discovered optical
isomers. Because of this property, Pasteur thought that these processes were catalysed by
specific microorganisms. He discovered that there were yeast cells involved with the production
of alcohol. He proved the role of microorganisms in fermentation. He also discovered other
growth in his medium. This introduced him to experiments of spontaneous generation; life arose
spontaneously. Pasteur found that heating kept something form putrefying (with swan neck
bottle). This settled the spontaneous generation controversy for ever.
Heat treatment is used in the food industry as pasteurization. Pasteur also made vaccines.
1.10 Koch provided experimental support to the germ theory of infectious diseases. He
discovered, with mice, that anthrax could grow outside the
host in a medium. He formulated some criteria, Koch’s
postulates (see image). The second step, growing in an
isolated culture, means that a culture is pure. Petri
discovered the Petri disk, which became the tool for this
research. Koch discovered that classification of bacteria was
equal to that of larger organisms.
, Koch discovered the contagious agent of tuberculosis. He succeeded in growing cultures of these
bacteria.
1.11 Martinus Beijerinck contributed in the field of microbiology with the formulation of
enrichment culture technique. This means that microorganisms are isolated in highly specific
mediums. Sergei Winogradsky isolated several notable bacteria (such as nitrogen and sulphur
bacteria). He showed chemolithotrophy; to oxidation of inorganic compounds to yield energy.
He showed that these microorganisms were widespread in the nature.
1.12 Kluyver discovered that, even though their differences, microorganisms use the same
biochemical pathways. Certain macromolecules and biochemical reactions are universal. The
hunt for the molecular basis of heredity began with an experiment by Griffith. He discovered that
a certain strain could be transformed to another strain, so genetic information must have been
transferred. The Avery-MacLeod-McCarty experiment showed that this transferring was DNA.
This proved that DNA is the genetic material of cells. Watson and Crick discovered the structure
of DNA with Xray images by Franklin. Zuckerlandl and Pauling discovered that we can use DNA
to reconstruct evolutionary relationships.
1.13 Ribosomal RNA revolutionized the understanding of microbial evolution. Darwin’s tools of
palaeontology were useless for microorganisms, because microorganisms do not leave fossils.
Haeckel did the first attempt and suggested that single-cells were ancestral to other forms of life.
Witthaker proposed a five kingdom classification. With the theory of DNA, everything changed.
Woese discovered the function of ribosomal RNA. These are universally distributed, functionally
constant, highly conservative and of adequate length. He compared rRNA sequences and
discovered archaea and connections between different forms of life. The tree of life is a
phylogenetic tree, a diagram that predicts the evolutionary history, phylogeny.
Pace discovered that rRNA could be directly isolated from the environment.
1.14 Bacteria have a prokaryotic structure. They tremendously diverse in appearance and
function. Among them, 30 major phylogenetic lineages have been described. An analysis of rRNA
reveals at least 80 bacterial phyla.
Archaea have also a prokaryotic cell structure. Cultured isolation shows less diversity then
bacteria. It consists of five phyla. They are common in extreme conditions but they’re found
widely in nature. This domain lacks any known pathogens or parasites of plants and animals.
Eukaryotes consists of plants, animals and fungi. These group is relatively young, 600 million
years old. The first were unicellular microbes. These occurred 2 billion years ago for the first
time. There at least six kingdoms. They vary drastically in size, shape and physiology.
Viruses are not in the tree of life. They are parasites who can only replicate inside a host cell.
They take over metabolic systems, but do not carry out metabolic processes themselves. They
have genomes of DNA or RNA. They can infect cells of all domains. Bacteriophages have been
used as model systems to explore aspects of viral biology.
Chapter 2
2.1 Morphology means the shape of a cell. A spherical or ovoid cell is a coccus, rods are staves
cylindrical cell a bacillus and spiral shaped a spirilla. Some cells form clusters, like chains with cocci.
Many variations is sizes are known. Morphology is a poor predictor for other properties of a cell.
Nevertheless, its morphology is an important property. We know little about why a cell is shaped like
it is. Pleomorphism is the property to change shape with changing environmental properties.
2.2 Most rods are between 0.5 and 4 μm. The range for prokaryotes is 0.2-700 μm. Some are very
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