MCB 211 Note
MCB 211 Note
The science of microbiology revolves around two interconnected themes: (1) understanding the
living world of microscopic organisms, and (2) applying our understanding of microbial life
processes for the benefit of humankind and planet Earth.
As a basic biological science, microbiology uses and develops tools for probing the fundamental
processes of life. Scientists have obtained a rather sophisticated understanding of the chemical
and physical basis of life from studies of microorganisms because microbial cells share many
characteristics with cells of multicellular organisms; indeed, all cells have much in common. But
unlike plants and animals, microbial cells can be grown to extremely high densities in small-
scale laboratory cultures, making them readily amenable to rapid biochemical and genetic study.
Collectively, these features make microorganisms excellent experimental systems for
illuminating life processes common to multicellular organisms, including humans.
Although microorganisms are the smallest forms of life, collectively they constitute the bulk of
biomass on Earth and carry out many necessary chemical reactions for higher organisms. In the
absence of microorganisms, higher life forms would never have evolved and could not now be
sustained. Moreover, humans, plants, and animals are intimately tied to microbial activities for
the recycling of key nutrients and for degrading organic matter. It is safe to say that no other life
forms are as important as microorganisms for the support and maintenance of life on Earth.
Microorganisms existed on Earth for billions of years before plants and animals appeared, and
we will see later that the genetic and physiological diversity of microbial life greatly exceeds that
of the plants and animals. This huge diversity accounts for some of the spectacular properties of
microorganisms.
Microbial Cells
A basic tenet of biology is that the cell is the fundamental unit of life. A single cell is an entity
isolated from other such entities by a membrane; many cells also have a cell wall outside the
membrane. The membrane defines the compartment that is the cell, maintains the correct
proportions of internal constituents, and prevents leakage, while the wall lends structural strength
to the cell. But the fact that a cell is a compartment does not mean that it is a sealed
compartment. Instead, the membrane is semipermeable and thus the cell is an open, dynamic
structure. Cells can communicate, move about, and exchange materials with their environments,
and so they are constantly undergoing change.
In nature, microbial cells live in populations in association with populations of cells of other
species. A population is a group of cells derived from a single parental cell by successive cell
divisions. The immediate environment in which a microbial population lives is called its habitat.
Populations of cells interact with other populations in microbial communities. The diversity and
abundance of microorganisms in microbial communities is controlled by the resources (foods)
and conditions (temperature, pH, oxygen content, and so on) that prevail in their habitat.
Microbial populations interact with each other in beneficial, neutral, or harmful ways. For
example, the metabolic waste products of one group of organisms can be nutrients or even
poisons to other groups of organisms. Habitats differ markedly in their characteristics, and a
habitat that is favorable for the growth of one organism may actually be harmful for another.
Collectively, we call all the living organisms, together with the physical and chemical
components of their environment, an ecosystem. Major microbial ecosystems are aquatic
(oceans, ponds, lakes, streams, ice, hot springs), terrestrial (surface soils, deep subsurface), and
other organisms, such as plants and animals.
An ecosystem is greatly influenced and in some cases even controlled by microbial activities.
Microorganisms carrying out metabolic processes remove nutrients from the ecosystem and use
them to build new cells. At the same time, they excrete waste products back into the
environment. Thus, microbial ecosystems expand and contract, depending on the resources and
conditions available. Over time, the metabolic activities of microorganisms gradually change
their ecosystems, both chemically and physically. For example, molecular oxygen (O2) is a vital
nutrient for some microorganisms but a poison to others. If aerobic (oxygen-consuming)
microorganisms remove O2 from a habitat, rendering it anoxic (O 2 free), the changed conditions
may favor the growth of anaerobic microorganisms that were formerly present in the habitat but
unable to grow. In other words, as resources and conditions change in a microbial habitat, cell
populations rise and fall, changing the habitat once again.
Microorganisms were the first entities on Earth with the properties of living systems, and we will
see that a particular group of microorganisms called the cyanobacteria were pivotal in biological
evolution because oxygen (O2)—a waste product of their metabolism—prepared planet Earth for
more complex life forms.
The First Cells and the Onset of Biological Evolution
How did cells originate? Were cells as we know them today the first self-replicating structures
on Earth? Because all cells are constructed in similar ways, it is thought that all cells have
descended from a common ancestral cell, the last universal common ancestor (LUCA). After the
first cells arose from nonliving materials, a process that occurred over hundreds of millions of
years, their subsequent growth formed cell populations, and these then began to interact with
other populations in microbial communities. Evolution selected for improvements and
diversification of these early cells to eventually yield the highly complex and diverse cells we
see today.
Life on Earth through the Ages Earth is 4.6 billion years old. Scientists have evidence that cells
first appeared on Earth between 3.8 and 3.9 billion years ago, and these organisms were
exclusively microbial. In fact, microorganisms were the only life on Earth for most of its history.
Gradually, and over enormous periods of time, more complex organisms appeared. What were
some of the highlights along the way?
During the first 2 billion years or so of Earth’s existence, its atmosphere was anoxic; O 2 was
absent, and nitrogen (N2), carbon dioxide (CO2), and a few other gases were present. Only
microorganisms capable of anaerobic metabolisms could survive under these conditions, but
these included many different types of cells, including those that produce methane, called
methanogens. The evolution of phototrophic microorganisms—organisms that harvest energy
from sunlight—occurred within a billion years of the formation of Earth. The first phototrophs
were relatively simple ones, such as purple bacteria and other anoxygenic (non-oxygenevolving)
phototrophs, which are still widespread in anoxic habitats today. Cyanobacteria (oxygenic, or
oxygen-evolving, phototrophs) evolved from anoxygenic phototrophs nearly a billion years later
and began the slow process of oxygenating the atmosphere. Triggered by increases in O 2 in the
atmosphere, multicellular life forms eventually evolved and continued to increase in complexity,
culminating in the plants and animals we know today.
The events that unfolded beyond LUCA led to the evolution of three major lineages of microbial
cells, the Bacteria, the Archaea, and the Eukarya; microbial Eukarya were the ancestors of the
plants and animals.
How do we know? Microbiology in perspective: to the ‘golden age’ and beyond
We have learnt an astonishing amount about the invisible world of microorganisms, particularly
over the last century and a half. How has this happened? The penetrating insights of brilliant
individuals are rightly celebrated, but a great many ‘breakthroughs’ or ‘discoveries’ have only
been made possible thanks to some (frequently unsung) development in microbiological
methodology. For example, on the basis that ‘seeing is believing’, it was only when we had the
means to see microorganisms under a microscope that we could prove their existence.
Microorganisms had been on the Earth for some 4000 million years, when Antoni van
Leeuwenhoek started out on his pioneering microscope work in 1673. Leeuwenhoek was an
amateur scientist who spent much of his spare time grinding glass lenses to produce simple
microscopes. His detailed drawings make it clear that the ‘animalcules’ he observed from a
variety of sources included representatives of what later became known as protozoa, bacteria and
fungi. Where did these creatures come from? Arguments about the origin of living things
revolved around the long held belief in spontaneous generation, the idea that living organisms
could arise from non-living matter.
In an elegant experiment, the Italian Francesco Redi (1626–1697) showed that the larvae found
on putrefying meat arose from eggs deposited by flies, and not spontaneously as a result of the
decay process. This can be seen as the beginning of the end for the spontaneous generation
theory, but many still clung to the idea, claiming that while it may not have been true for larger
organisms, it must surely be so for minute creatures such as those demonstrated by
Leeuwenhoek. Despite mounting evidence against the theory, as late as 1859, fresh ‘proof’ was
still being brought forward in its support.
Enter onto the scene Louis Pasteur (1822–1895), still arguably the most famous figure in the
history of microbiology. Pasteur trained as a chemist, and made a lasting contribution to the
science of stereochemistry before turning his attention to spoilage problems in the wine industry.
He noticed that when lactic acid was produced in wine instead of alcohol, rod-shaped bacteria
were always present, as well as the expected yeast cells. This led him to believe that while the
yeast produced the alcohol, the bacteria were responsible for the spoilage, and that both types of
organism had originated in the environment. Exasperated by continued efforts to substantiate the
theory of spontaneous generation, he set out to disprove it once and for all.
In response to a call from the French Academy of Science, he carried out a series of experiments
that led to the acceptance of biogenesis, the idea that life arises only from already existing life.
Using his famous swam-necked flasks, he demonstrated in 1861 that as long as dust particles
(and the microorganisms carried on them) were excluded, the contents would remain sterile. This
also disproved the idea held by many that there was some element in the air itself that was
capable of initiating microbial growth. In Pasteur’s words ‘the doctrine of spontaneous
generation will never recover from this mortal blow. There is no known circumstance in which it
can be affirmed that microscopic beings came into the world without germs, without parents
similar to themselves.’ Pasteur’s findings on wine contamination led inevitably to the idea that
microorganisms may be also be responsible for diseases in humans, animals and plants.
Figure 2: Pasteur’s swam-necked flasks. Broth solutions rich in nutrients were placed in flasks
and boiled. The necks of the flasks were heated and drawn out into a curve, but kept open to the
atmosphere. Pasteur showed that the broth remained sterile because any contaminating dust and
microorganisms remained trapped in the neck of the flask as long as it remained upright.
The notion that some invisible (and therefore, presumably, extremely small) living creatures
were responsible for certain diseases was not a new one. Long before microorganisms had been
shown to exist, the Roman philosopher Lucretius (∼98–55 bc) and much later the physician
Girolamo Fracastoro (1478–1553) had supported the idea. Fracastoro wrote ‘Contagion is an
infection that passes from one thing to another’ and recognised three forms of transmission: by
direct contact, through inanimate objects and via the air. We still class transmissibility of
infectious disease in much the same way today. The prevailing belief at the time, however, was
that an infectious disease was due to something called a miasma, a poisonous vapour arising
from dead or diseased bodies, or to an imbalance between the four humours of the body (blood,
phlegm, yellow bile and black bile).
During the 19th century, many diseases were shown, one by one, to be caused by
microorganisms. In 1835, Agostino Bassi showed that a disease of silkworms was due to a
fungal infection, and 10 years later, Miles Berkeley demonstrated that a fungus was also
responsible for the great Irish potato blight. Joseph Lister’s pioneering work on antiseptic
surgery provided strong, albeit indirect, evidence of the involvement of microorganisms in
infections of humans. The use of heat-treated instruments and of phenol both on dressings and
actually sprayed in a mist over the surgical area, was found greatly to reduce the number of
fatalities following surgery. Around the same time, in the 1860s, the indefatigable Pasteur had
shown that a parasitic protozoan was the cause of another disease of silkworms called pebrine´,
which had devastated the French silk industry.
The first proof of the involvement of bacteria in disease and the definitive proof of the germ
theory of disease came from the German Robert Koch. In 1876 Koch showed the relationship
between the cattle disease anthrax and a bacillus which we now know as Bacillus anthracis.
Koch infected healthy mice with blood from diseased cattle and sheep, and noted that the
symptoms of the disease appeared in the mice, and that rod shaped bacteria could be isolated
from their blood. These could be grown in culture, where they multiplied and produced spores.
Injection of healthy mice with these spores (or more bacilli) led them too to develop anthrax and
once again the bacteria were isolated from their blood. These results led Koch to formalise the
criteria necessary to prove a causal relationship between a specific disease condition and a
particular microorganism.
Koch’s greatest achievement was in using the advances in methodology and the principles of his
own postulates to demonstrate the identity of the causative agent of tuberculosis, which at the
time was responsible for around one in every seven human deaths in Europe. Although it was
believed by many to have a microbial cause, the causative agent had never been observed, either
in culture or in the affected tissues. We now know that Mycobacterium tuberculosis (the tubercle
bacillus) is very difficult to stain by conventional methods due to the high lipid content of the
cell wall surface. Koch developed a staining technique that enabled it to be seen, but realised that
in order to satisfy his own postulates, he must isolate the organism and grow it in culture.
Figure 3: Diagrammatic illustration of Koch’s postulate
The development of pure cultures revolutionised microbiology, and within the next 30 years or
so, the pathogens responsible for the majority of common human bacterial diseases had been
isolated and identified. Not without just cause is this period known as the ‘golden age’ of
microbiology!
Most microbes are unicellular and small enough that they require artificial magnification to be
seen. However, there are some unicellular microbes that are visible to the naked eye, and some
multicellular organisms that are microscopic. An object must measure about 100 micrometers
(µm) to be visible without a microscope, but most microorganisms are many times smaller than
that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but
is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller
than bacteria (Figure 4). See Table 1 for units of length used in microbiology.
Figure 4: The relative sizes of various microscopic and nonmicroscopic objects. Note that a
typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 µm), which
is at least 10 times smaller than a typical plant or animal cell (~10–100 µm). An object must
measure about 100 µm to be visible without a microscope.
Microorganisms differ from each other not only in size, but also in structure, habitat,metabolism,
and many other characteristics. While we typically think of microorganisms as being unicellular,
there are also many multicellular organisms that are too small to be seen without a microscope.
Some microbes, such as viruses, are even acellular (not composed of cells).Microorganisms are
found in each of the three domains of life: Archaea, Bacteria, and Eukarya. Microbes within the
domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes
in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as
viruses, do not fall within any of the three domains of life. In this section, we will briefly
introduce each of the broad groups of microbes. Later chapters will go into greater depth about
the diverse species within each group.
Prokaryotic Microorganisms
Bacteria are found in nearly every habitat on earth, including within and on humans. Most
bacteria are harmless or helpful, but some are pathogens, causing disease in humans and other
animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a
true nucleus. Most bacteria have cell walls that contain peptidoglycan. Bacteria are often
described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped
(bacillus), or curved (spirillum, spirochete, or vibrio). Figure 5 shows examples of these shapes.
Figure 5: Common bacterial shapes. Note how coccobacillus is a combination of spherical
(coccus) and rod-shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney
Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work
by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for
Disease Control and Prevention)
They have a wide range of metabolic capabilities and can grow in a variety of environments,
using different combinations of nutrients. Some bacteria are photosynthetic, such as
oxygenic cyanobacteria and anoxygenic green sulfur and green nonsulfur bacteria; these
bacteria use energy derived from sunlight, and fix carbon dioxide for growth. Other types of
bacteria are nonphotosynthetic, obtaining their energy from organic or inorganic compounds in
their environment.
Archaea are also unicellular prokaryotic organisms. Archaea and bacteria have different
evolutionary histories, as well as significant differences in genetics, metabolic pathways, and the
composition of their cell walls and membranes. Unlike most bacteria, archaeal cell walls do not
contain peptidoglycan, but their cell walls are often composed of a similar substance called
pseudopeptidoglycan. Like bacteria, archaea are found in nearly every habitat on earth, even
extreme environments that are very cold, very hot, very basic, or very acidic. Some archaea live
in the human body, but none have been shown to be human pathogens.
Eukaryotic Microorganisms
The domain Eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as
protists, fungi, plants, and animals. The major defining characteristic of eukaryotes is that their
cells contain a nucleus.
Protists are unicellular eukaryotes that are not plants, animals, or fungi. Algae and protozoa are
examples of protists.
Algae (singular: alga) are plant-like protists that can be either unicellular or multicellular. Their
cells are surrounded by cell walls made of cellulose, a type of carbohydrate. Algae are
photosynthetic organisms that extract energy from the sun and release oxygen and carbohydrates
into their environment. Because other organisms can use their waste products for energy, algae
are important parts of many ecosystems. Many consumer products contain ingredients derived
from algae, such as carrageenan or alginic acid, which are found in some brands of ice cream,
salad dressing, beverages, lipstick, and toothpaste. A derivative of algae also plays a prominent
role in the microbiology laboratory. Agar, a gel derived from algae, can be mixed with various
nutrients and used to grow microorganisms in a Petri dish. Algae are also being developed as a
possible source for biofuels.
Protozoa (singular: protozoan) are protists that make up the backbone of many food webs by
providing nutrients for other organisms. Protozoa are very diverse. Some protozoa move with
help from hair-like structures called cilia or whip-like structures called flagella. Others extend
part of their cell membrane and cytoplasm to propel themselves forward. These cytoplasmic
extensions are called pseudopods (“false feet”). Some protozoa are photosynthetic; others feed
on organic material. Some are free-living, whereas others are parasitic, only able to survive by
extracting nutrients from a host organism. Most protozoa are harmless, but some are pathogens
that can cause disease in animals or humans.
Fungi (singular: fungus) are also eukaryotes. Some multicellular fungi, such as mushrooms,
resemble plants, but they are actually quite different. Fungi are not photosynthetic, and their cell
walls are usually made out of chitin rather than cellulose.Unicellular fungi—yeasts—are
included within the study of microbiology. There are more than 1000 known species. Yeasts are
found in many different environments, from the deep sea to the human navel. Some yeasts have
beneficial uses, such as causing bread to rise and beverages to ferment; but yeasts can also cause
food to spoil. Some even cause diseases, such as vaginal yeast infections and oral thrush.
Other fungi of interest to microbiologists are multicellular organisms called molds. Molds are
made up of long filaments that form visible colonies. Molds are found in many different
environments, from soil to rotting food to dank bathroom corners. Molds play a critical role in
the decomposition of dead plants and animals. Some molds can cause allergies, and others
produce disease-causing metabolites called mycotoxins. Molds have been used to make
pharmaceuticals, including penicillin, which is one of the most commonly prescribed antibiotics,
and cyclosporine, used to prevent organ rejection following a transplant.
Helminths: Multicellular parasitic worms called helminths are not technically microorganisms,
as most are large enough to see without a microscope. However, these worms fall within the field
of microbiology because diseases caused by helminths involve microscopic eggs and larvae. One
example of a helminth is the guinea worm, or Dracunculus medinensis, which causes dizziness,
vomiting, diarrhea, and painful ulcers on the legs and feet when the worm works its way out of
the skin. Infection typically occurs after a person drinks water containing water fleas infected by
guinea-worm larvae. In the mid-1980s, there were an estimated 3.5 million cases of guinea-worm
disease, but the disease has been largely eradicated. In 2014, there were only 126 cases reported,
thanks to the coordinated efforts of the World Health Organization (WHO) and other groups
committed to improvements in drinking water sanitation.
Viruses are acellular microbial agents, which means they are not composed of cells. Essentially,
a virus consists of proteins and genetic material—either DNA or RNA, but never both—that are
inert outside of a host organism. However, by incorporating themselves into a host cell, viruses
are able to co-opt the host’s cellular mechanisms to multiply and infect other hosts.Viruses can
infect all types of cells, from human cells to the cells of other microorganisms. In humans,
viruses are responsible for numerous diseases, from the common cold to deadly Ebola. However,
many viruses do not cause disease.
Viruses are infectious agents with both living and nonliving characteristics. They can infect
animals, plants, and even other microorganisms. Viruses that infect only bacteria are called
bacteriophages and those that infect only fungi are termed mycophages. There are even some
viruses called virophages that infect other viruses.
a. They reproduce at a. They are acellular, that is, they contain no cytoplasm or
a fantastic rate, but cellular organelles.
only in living host b. They carry out no metabolism on their own and must
cells. replicate using the host cell's metabolic machinery. In other
b. They can mutate. words, viruses don't grow and divide. Instead, new viral
components are synthesized and assembled within the
infected host cell.
c. The vast majority of viruses possess either DNA or RNA
but not both.
Recently, viruses have been declared as living entities based on the large number of protein folds
encoded by viral genomes that are shared with the genomes of cells. This indicates that viruses
likely arose from multiple ancient cells.
The vast majority of viruses contain only one type of nucleic acid: DNA or RNA, but not both.
Virus are totally dependent on a host cell for replication (i.e., they are strict intracellular
parasites.) Furthermore, viral components must assemble into complete viruses (virions) to go
from one host cell to another. Since viruses lack metabolic machinery of their own and are
totally dependent on their host cell for replication, they cannot be grown in synthetic culture
media. Animal viruses are normally grown in animals, embryonated eggs, or in cell cultures
where in anima,l host cells are grown in a synthetic medium and the viruses are then grown in
these cells.
Structure Most bacteria consist of They consist of little more than A typical fungus consists of
a ring of DNA a small piece of genetic the hyphae, which form the
surrounded by a cellular material surrounded by a thin fungal body. These hyphae
machinery, contained protein coating. Some are also are microscopic walled
within a fatty surrounded by a thin and fatty tubes or filaments that are
membrane. envelop. lined with plasma
membrane and contain
cytoplasm.
Cocci = sphere shape icosahedral, some are helical like strands, called hyphae
Shape
shaped. (collectively called
Bacilli = rod shape mycelium)
Some viruses are shaped like a
Spirella = spiral shape space ship. They are called
bacteriophages.
Source of Energy Seize energy from the Seize materials and energy They use pre-existing
carbon sources in their
same essential sources environment and use the
as humans, including from host cells by hijacking energy from chemical
sugars, proteins, and cellular machinery reactions to create the
fats. organic compounds they
need for energy and growth.
On the other hand, Virus is a mobile genetic material that is enclosed in a protein or a fatty
(0.1 to 0.3 microns) in size. They were discovered just before 1900, and were known as filterable
viruses, due to their small size. A debatable issue is regarding their status as living or non living
entities. This is due to the fact that they consist of merely nucleic acid that is wrapped in a coat
of protein.