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Summary Microbiology
- Vak
- AB_1276
- Instelling
- Vrije Universiteit Amsterdam (VU)
Microbiology notes directly from the lectures and course material, integration with laboratory practicals and workgroups.
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MICROBIOLOGYMODULE 1
Microorganisms typically live in complex microbial communities and their activities are
regulated by interactions with each other, with their environments, and with other organisms.
Microorganisms represent a major fraction of Earth’s biomass, and their activities are
essential to sustaining life. Indeed, the very oxygen (O2) we breathe is the result of microbial
activities. Plants and animals are immersed in a world of microbes, and their evolution and
survival are heavily influenced by microbial activities, by microbial symbioses, and by
pathogens—those microbes that cause disease.
The cultivation of microorganisms is also foundational to microbiology. A microbial culture is
a collection of cells that have been grown in or on a nutrient medium. A medium (plural,
media) is a liquid or solid nutrient mixture that contains all of the nutrients required for a
microorganism to grow. In microbiology, we use the word growth to refer to the increase in
cell number as a result of cell division. A single microbial cell placed on a solid nutrient
medium can grow and divide into millions or even billions of cells that form a visible colony.
Elements of Microbial Structure: All cells have a permeability barrier called the
cytoplasmic membrane that separates the inside of the cell, the cytoplasm, from the outside.
The cytoplasm is an aqueous mixture of macromolecules (for example proteins, lipids,
nucleic acids, and polysaccharides), small organic molecules (mostly the precursors of
macromolecules), various inorganic ions, and ribosomes. All cells also contain ribosomes,
which are the structures responsible for protein synthesis. Some cells have a cell wall that
lends structural strength to a cell. The cell wall is a relatively permeable structure located
outside the cytoplasmic membrane and is a much stronger layer than the membrane itself.
Cell walls are typically found in plant cells and most microorganisms but are not found in
animal cells. Cells having eukaryotic cell structure are found in a group of organisms called
the Eukarya. This group includes plants and animals as well as diverse microbial eukaryotes
such as algae, protozoa, and fungi. Prokaryotic cell structure is found within two different
groups of organisms we know as Bacteria and Archaea. Prokaryotic cells have few internal
structures, they lack a nucleus, and they typically lack organelles . Bacteria and Archaea
appeared long before the evolution of eukaryotes. Archaea and Eukarya are more similar to
each other than either is to Bacteria.
Genomes: The genomes of Bacteria and Archaea are typically closed circular
chromosomes (though some prokaryotic cells have linear chromosomes). The chromosome
aggregates within the prokaryotic cell to form the nucleoid, a mass that is visible in the
electron microscope (Figure 1.4a) but which is not enclosed by a membrane. Plasmids
typically contain genes that are not essential but often confer some special property on the
cell The genomes of Bacteria and Archaea are typically small and compact, and most
contain between 500 and 10,000 genes encoded by 0.5 to 10 million base pairs of DNA.
Eukaryotic cells typically have much larger and much less streamlined genomes than
prokaryotic cells. A human cell, for example, contains approximately 3 billion base pairs,
which encode about 20,000–25,000 genes.
Microorganisms have the ability to sense and respond to changes in their local environment.
Many microbial cells are capable of motility, typically by self-propulsion (Figure 1.5). Motility
allows cells to relocate in response to environmental conditions. Some microbial cells
undergo differentiation, which may result in the formation of modified cells specialized for
growth, dispersal, or survival. Many prokaryotic cells can also exchange genes with
neighboring cells, regardless of their species, in the process of horizontal gene transfer.
,Evolution results when genes in a population of cells change in sequence and frequency
over time, leading to descent with modification. The evolution of microorganisms can be very
rapid relative to the evolution of plants and animals. For example, the indiscriminate use of
antibiotics in humans. The rapid pace of microbial evolution can be attributed in part to the
ability of microorganisms to grow very quickly and to acquire new genes through the process
of horizontal gene transfer.
Morphology: defined by cell size and shape. The unaided human eye has difficulty
resolving objects that are less than 100 micom in diameter, but this is the scale of the
microbial world. Most prokaryotic cells are small, ranging between 0.5 and 10 microm in
length, but prokaryotic cells can vary widely in size. For example, the smallest prokaryotic
cells are about 0.2 microm in diameter and the largest can be more than 600 mim long.
Epulopiscium fishelsoni and Thiomargarita namibiensis, a large sulfur chemolithotroph and
currently the largest known of all prokaryotic cells. Cell widths vary from 400 to 750 μm.
Prokaryotic cells, in contrast, rely on diffusion for transport through the cytoplasm and this
limits their size. While diffusion is very fast at small distances, the rate of diffusion increases
as the square of the distance traveled. Hence, the metabolic rate in a prokaryotic cell varies
inversely with the square of its size. Since diffusion is rapid at small spatial scales, high
metabolic rates can be maintained in small prokaryotic cells without a need for complex
cellular structures. Ultimately, the lower limit to cell size is likely a function of the amount of
space needed to house the essential biochemical components—proteins, nucleic acids,
ribosomes and so on (Section 1.2)—that all cells need to survive and reproduce.
The S/V ratio: The volume of a sphere is a function of the cube of its radius (V = 4 3pr 3),
whereas its surface area is a function of the square of the radius (S = 4πr 2). Therefore, the
S/V ratio of a coccus is 3/r. The S/V ratio of a cell controls many of its properties, including
how fast it grows (its growth rate) and shape. Cellular growth rate depends in part on the
rate at which cells exchange nutrients and waste products with their environment. As cell
size decreases, the S/V ratio of the cell increases, and this means that small cells can
exchange nutrients and wastes more rapidly.
Shapes: Common morphologies of prokaryotic cells are shown in Figure 1.8. A cell that is
spherical or ovoid in morphology is called a coccus (plural, cocci). A cylindrically shaped cell
is called a rod or a bacillus (plural, bacilli). A spiral-shaped cell is called a spirillum (plural,
spirilla). A cell that is slightly curved and comma-shaped is called a vibrio. A spirochete is a
special kind of organism that has a spiral shape but which differs from spirilla because the
cells of spirochetes are flexible, whereas cells of spirilla are rigid. Some bacteria are irregular
in shape. Appendages, such as stalks and hyphae, are used by some cells for attachment or
to increase surface area. In addition, asymmetrical cell division such as budding can result in
irregular and asymmetrical cell shapes. Some cocci occur in pairs (diplococci), some form
long chains (streptococci), others occur in three-dimensional cubes (tetrads or sarcinae),
and still others occur in grapelike clusters (staphylococci). Filamentous bacteria are long,
thin, rod-shaped bacteria that divide terminally and then form long filaments composed of
many cells attached end to end.
DOMAINS: all known cellular organisms belong to one of these three domains.
Bacteria: Bacteria have a prokaryotic cell structure (Figure 1.4a). Bacteria are often thought
of as undifferentiated single cells with a length that ranges from 0.5 to 10 microm. While
bacteria that fit this description are common, the Bacteria are actually tremendously diverse
in appearance, size, and function (Figure 1.9). Although most bacteria are unicellular, some
bacteria can differentiate to form multiple cell types and others are even multicellular.
,More than 90% of cultivated bacteria belong to one of only four phyla: Actinobacteria,
Firmicutes, Proteobacteria, and Bacteroidetes. The analyses of environmental DNA
sequences provide evidence for the existence of at least 80 bacterial phyla (phylogenetic
lineages).
Archaea: Archaea also have a prokaryotic cell structure (Figure 1.4a). The domain Archaea
consists of five described phyla: Euryarchaeota, Crenarchaeota (mostly these two)
Thaumarchaeota, Nanoarchaeota, and Korarchaeota, but analysis of environmental DNA
sequences indicate more than 12 archaeal phyla likely exist. Archaea have historically been
associated with extreme environments, some species of Archaea hold many of the records
that define the chemical and physical limits of life as we know them. Archaea are also
notable in that this domain lacks any known disease-causing (pathogenic or parasitic)
species of plants or animals.
Eukarya: Plants, animals, and fungi are the most well-known groups of Eukarya. These
groups are phylogenetically relatively young compared with Bacteria and Archaea,
originating during an evolutionary burst called the Cambrian explosion, which began about
600 million years ago. The first eukaryotes, however, were unicellular microbes. Microbial
eukaryotes, which include diverse algae and protozoa, may have first appeared as early as 2
billion years ago. There are at least six kingdoms (phyla) of Eukarya. Among the smallest
are the nanoflagellates, while the largest single-celled organisms are eukaryotes, but they
are hardly microbial.
Viruses: Although viruses can replicate—a hallmark of cells—viruses are obligate parasites
that can only replicate within the cytoplasm of a host cell. Viruses are not cells, and they lack
the cytoplasmic membrane, cytoplasm, and ribosomes found in all forms of cellular life.
Viruses do not carry out metabolic processes; instead, they take over the metabolic systems
of infected cells and turn them into vessels for producing more viruses. Viruses have
genomes composed of DNA or RNA that can be either double- or single-stranded. Viral
genomes are often quite small, with the smallest having only three genes. Different viruses
are known to infect cells from all three domains of life. Viruses are often classified on the
basis of their structure, genome composition, and host specificity. Viruses that infect bacteria
are called bacteriophages (or phages, for short). While most viruses are considerably
smaller than bacterial cells, there are also unusually large viruses such as the
Pandoraviruses, which can be more than 1 micrometer long and have a genome that
contains as many as 2500 genes, larger than that of many bacteria.
HISTORY OF LIFE: Earth is about 4.6 billion years old, and microbial cells first appeared
between 3.8 and 4.3 billion years ago. During the first 2 billion years of Earth’s existence, its
atmosphere was anoxic (O2 was absent), and only nitrogen (N2), carbon dioxide (CO2), and
a few other gases were present. Only microorganisms capable of anaerobic metabolism
(that is, metabolisms that do not require O2) could survive under these conditions. The
evolution of phototrophic microorganisms—organisms that harvest energy from
sunlight—occurred within 1 billion years of the formation of Earth. The first phototrophs were
anoxygenic (non-oxygen-producing), Cyanobacteria, oxygen-producing (oxygenic)
phototrophs, evolved nearly a billion years later. After the oxygenation of Earth’s
atmosphere, multicellular life forms eventually evolved, culminating in the plants and animals
we know today. 80% of life’s history was exclusively microbial, and thus in many ways, Earth
can be considered a microbial planet. As evolutionary events unfolded, three major lineages
of microbial cells—the Bacteria, the Archaea, and the Eukarya— were distinguished. All
cellular organisms share certain characteristics and as a result, certain genes are found in all
, cells. For example, approximately 60 genes are universally present in cells of all three
domains. Examination of these genes reveals that all three domains have descended from a
common ancestor, the last universal common ancestor (LUCA).
There are an estimated 2x10^30 microbial cells on Earth. The total amount of carbon
present in all microbial cells is a significant fraction of Earth’s biomass (Figure 1.12).
Moreover, the total amount of nitrogen and phosphorus (essential nutrients for life) within
microbial cells is almost four times that in all plant and animal cells combined. Microbes also
represent a major fraction of the total DNA in the biosphere (about 31%), and their genetic
diversity far exceeds that of plants and animals. Microbes are even abundant in habitats that
are much too harsh for other forms of life, extremophiles, and their properties define the
physiochemical limits to life as we know it. All ecosystems are influenced to one extent or
another by microbial activities. The metabolic activities of microorganisms can change the
habitats in which they live, both chemically and physically, and these changes can affect
other organisms. Within the human body, for example, more microbial cells can be present
than human cells, and more than 200 microbial genes are present for every human gene.
These microbes provide benefits and services that are essential to human health.
The Impact of Microorganisms on Human Society: At the beginning of the twentieth
century, more than half of all humans died from infectious diseases caused by bacterial and
viral pathogens. Today, however, infectious diseases are largely preventable due to
advances in our understanding of microbiology. Infectious diseases now cause fewer than
5% of all deaths in countries where interventions, made possible by microbiology, are readily
available. However, the World Health Organization has documented that they still account
for more than a third of all deaths in countries where microbial interventions are less
available, such as those having low-income economies.
Most microorganisms are beneficial, and in many cases are even essential to human
welfare and the functioning of the planet. Agriculture benefits from nutrient cycling performed
by microorganisms, in particular, the cycling of nitrogen, sulfur, and carbon compounds.
Bacteria regulate nutrient cycles (Figure 1.14), in soils and throughout the biosphere,
transforming and recycling the nutrients required by plants and animals. Ruminants, like
most animals, lack enzymes for breaking down the polysaccharide cellulose, the major
component of plant cell walls. The digestive tract of ruminants has a large specialized
chamber called the rumen in which cellulose is digested. The rumen contains a dense and
diverse community of microorganisms that digest and ferment cellulose. Ruminants
ultimately get their nutrition by metabolizing the waste products of microbial fermentation and
by digesting dead microbial cells. The human gastrointestinal (GI) tract lacks a rumen, but
we too rely on microbial partners for our nutrition. Human enzymes lack the ability to break
down complex carbohydrates (which can represent 10–30% of food energy) and so we rely
on our gut microbiome for this purpose. The colon, or large intestine (Figure 1.15), follows
the stomach and small intestine in the human digestive tract, and it contains about 1011
microbial cells per gram of colonic contents. Microbial cell numbers are low in the very acidic
(pH 2) stomach (about 104 per gram) but increase to about 108 per gram near the end of the
small intestine (pH 4–5) and then reach maximal numbers in the colon (pH 7).
Microbial growth in food can cause food spoilage and foodborne disease. The manner in
which we harvest and store food (for example, canning, refrigeration, drying, salting, etc.),
the ways in which we cook it, and even the spices we use, have all been fundamentally
influenced by the goal of eliminating harmful organisms from our food. But not all
microorganisms in foods are harmful, some beneficial microbes have been used for
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