Module 1
Introduction, Microscopes, Bacteria, and Archaea
Introduction to Microbes and Their Building Blocks
Microbiology is a specialized area of biology that deals with living things ordinarily too
small to be seen without magnification. Such microscopic organisms are collectively referred to
as microorganisms (my″-kroh-or′-gun-izms), microbes, or several other terms depending on the
kind of microbe or the purpose. There are several major groups of microorganisms that we’ll be
studying. They can be either cellular or noncellular. The cellular microorganisms we will study
are bacteria, archaea, fungi, and protozoa. Another cellular organism that causes human
infections is not technically a microorganism. Helminths are multicellular animals whose mature
form is visible to the naked eye. Acellular microorganisms causing human disease are the viruses
and prions. Table 1.1 gives you a first glimpse at these microorganisms. There is another very
important group of organisms called algae. They are critical to the health of the biosphere but do
not directly infect humans, so we will not consider them in this book. Each of the other seven
groups contains members that colonize humans, so we will focus on them.
The nature of microorganisms makes them both very easy and very difficult to study—
easy because they reproduce so rapidly and we can quickly grow large populations in the
laboratory, and difficult because we usually can’t see them directly. We rely on a variety of
indirect means of analyzing them in addition to using microscopes. For billions of years,
microbes have extensively shaped the development of the earth’s habitats and the evolution of
other life forms. It is understandable that scientists searching for life on other planets first look
for signs of microorganisms. Single-celled organisms appeared on this planet about 3.8 billion
years ago according to the fossil record.
One of these organisms—referred to as LCA, or the Last Common Ancestor—eventually
led to the appearance of two newer single cell types, called bacteria and archaea. A little bit later
this single-celled ancestor gave rise to eukaryotic (yoo-kar′-ee-ot-ic) cells. The type of cell
known as LCA no longer exists. Only its “offspring”—bacteria, archaea, and eukaryotes—
remain. Eukary means “true nucleus,” and these were the only cells containing a nucleus.
Bacteria and archaea have no true nucleus. For that reason, they have traditionally been called
prokaryotes (pro-kar′-ee-otes), meaning “prenucleus.” But researchers are suggesting we no
longer use the term prokaryote to lump them together because archaea and bacteria are so
distinct genetically. Some scientists have started calling them akaryotes, meaning “no nucleus.”
If you consider the seven types of microorganisms we will be dealing with in this book, you will
recognize bacteria and archaea as each having their own domain. The protozoa, fungi, and
helminths are all in the domain Eukarya. Viruses and prions do not appear on the tree of life
because they are not cells, and not considered living. That sounds strange, but we will delve into
that in the virus chapter, which comes later.
Figure 1.1 depicts the resulting tree of life—a diagram of all organisms on the planet.
There are two important things to note about this figure. First, all of biologic life falls into these
three categories, known as domains. Most of the organisms you are familiar with (animals,
plants, etc.) are in one category, Eukarya. Second, these three domains all emerged from a single
common cell type (the “stem” at the bottom).
Bacteria and archaea are predominantly single-celled organisms. Many eukaryotic
organisms are also single-celled, but the eukaryotic cell type also developed into highly complex
multicellular organisms such as worms and humans. In terms of numbers, eukaryotic cells are a
small minority compared to the bacteria and archaea, but their larger size (and our own status as
eukaryotes!) makes us perceive them as dominant to—and more important than—bacteria and
archaea.
Starting on the left, you see that the ancestor cell type was here alone for quite a while
before giving rise to the three domains of life. Eukaryotes came along last, and it took a very
long time for single-celled eukaryotes to develop into more complex eukaryotic organisms
(insects, reptiles, and mammals). On the scale pictured in the figure, humans just barely appeared
in very recent earth history. Bacteria and archaea preceded even the earliest animals by more
than 2 billion years. This is a good indication that humans are not likely to—nor should we try to
—eliminate bacteria from our environment. They have survived and adapted too many
catastrophic changes over the course of our geologic history.
Another indication of the huge influence bacteria exert is how ubiquitous they are.
Ubiquitous means “found everywhere.” Microbes can be found nearly everywhere, from deep in
the earth’s crust, to the polar ice caps and oceans, to inside the bodies of plants and animals.
Being mostly invisible, the actions of microorganisms are usually not as obvious or familiar as
those of larger plants and animals. They make up for their small size by their immense numbers
and by living in places that many other organisms cannot survive. Above all, they play central
roles in the earth’s landscape that are essential to life.
When we point out that single-celled organisms have adapted to a wide range of
conditions over the 3.5 billion years of their presence on this planet, we are talking about
evolution. The presence of life in its present form would not be possible if the earliest life forms
had not changed constantly, adapting to their environment and circumstances. Getting from the
far left in figure 1.2 to the far right, where humans appeared, involved billions and billions of
tiny changes, starting with the first cell that appeared about a billion years after the planet itself
was formed.
You have no doubt heard this concept described as the theory of evolution. Let’s clarify
some terms. Evolution is the accumulation of changes that occur in organisms as they adapt to
their environments. It is documented every day in all corners of the planet, an observable
phenomenon testable by science. Scientists use the term theory in a different way than the
general public does, which often leads to great confusion. In science, a theory begins as a
hypothesis, or an educated guess to explain an observation. By the time a hypothesis has been
labeled a theory in science, it has undergone years and years of testing and not been disproved. It
is taken as fact. This is much different from the common usage, as in “My theory is that he
overslept and that’s why he was late.” The theory of evolution, like the germ theory and many
other scientific theories, refers to a well-studied and well-established natural phenomenon, not
just a random guess.
Microbes are deeply involved in the flow of energy and food through the earth’s
ecosystems. Most people are aware that plants carry out photosynthesis, which is the light-fueled
conversion of carbon dioxide to organic material, accompanied by the formation of oxygen
(called oxygenic photosynthesis). However, bacteria invented photosynthesis long before the
first plants appeared, first as a process that did not produce oxygen (anoxygenic photosynthesis).
This anoxygenic photosynthesis later evolved into oxygenic photosynthesis, which not only
produced oxygen but also was much more efficient in extracting energy from sunlight. Hence,
these ancient, single-celled microbes were responsible for changing the atmosphere of the earth
from one without oxygen to one with oxygen. The production of oxygen also led to the use of
oxygen for aerobic respiration and the formation of ozone, both of which set off an explosion in
species diversification. Today, photosynthetic microorganisms (mainly bacteria and algae)
account for more than 70% of the earth’s photosynthesis, contributing the majority of the oxygen
to the atmosphere.
The temperature of the earth is regulated by gases emitted by living organisms. These
gases include carbon dioxide, nitrous oxide, and methane, which create an insulation layer in the
atmosphere and help retain heat. Many of these gases are produced by microbes living in the
environment and the digestive tracts of animals. The most abundant cellular organisms in the
oceans are not fish but bacteria. Think of a 2-liter soda bottle. Two liters of surface ocean water
contains approximately 1,000,000,000 (1 billion) bacteria. Each of these bacteria likely harbors
thousands of viruses inside of it, making viruses the most abundant inhabitants of the oceans.
The bacteria and their viruses are major contributors to photosynthesis and other important
processes that create our environment. (Be careful here. The first sentence in this paragraph said
that bacteria are the most abundant cellular organisms in oceans. But viruses, which are not
cellular, far outnumber them.) Bacteria and fungi live in complex associations with plants that
assist the plants in obtaining nutrients and water and may protect them against disease. Microbes
form similar interrelationships with animals, notably, in the stomach of cattle, where a rich
assortment of bacteria digests the complex carbohydrates of the animals’ diets and causes the
animals to release large amounts of methane into the atmosphere.
By accident or choice, humans have been using microorganisms for thousands of years to
improve life and even to shape civilizations. Baker’s and brewer’s yeasts are types of single-
celled fungi that cause bread to rise and ferment sugar into alcohol to make wine and beers.
Other fungi are used to make special cheeses such as Roquefort or Camembert. Historical
records show that households in ancient Egypt kept moldy loaves of bread to apply directly to
wounds and lesions. When humans manipulate microorganisms to make products in an industrial
setting, it is called biotechnology. For example, some specialized bacteria have unique capacities
to mine precious metals or to clean up human-created contamination. Genetic engineering is an
area of biotechnology that manipulates the genetics of microbes, plants, and animals for the
purpose of creating new products and genetically modified organisms (GMOs). One powerful
technique for designing GMOs is called recombinant DNA technology. This technology makes it
possible to transfer genetic material from one organism to another and to deliberately alter DNA.
Bacteria and fungi were some of the first organisms to be genetically engineered. This was
possible because they are single-celled organisms and they are so adaptable to changes in their
genetic makeup. Recombinant DNA technology has unlimited potential in terms of medical,
industrial, and agricultural uses.
Microbes can be engineered to synthesize desirable products such as drugs, hormones,
and enzymes. It has become popular to dislike GMOs. As with any technological advance, the
capacity to create GMOs can have both positive and negative aspects. Your job is to learn about
them, so that you can have an informed opinion. Another way of tapping into the unlimited
potential of microorganisms is the science of bioremediation (by′-oh-ree-mee-dee-ay″-shun).
This term refers to the ability of microorganisms— ones already present or those introduced
intentionally—to restore the stability of an ecosystem or to clean up toxic pollutants. Microbes
have a surprising capacity to break down chemicals that would be harmful to other organisms
(figure 1.4). This includes even human-made chemicals that scientists have developed and for
which there are no natural counterparts.
Microbes Harming Humans One of the most fascinating aspects of the microorganisms
with which we share the earth is that, despite all of the benefits they provide, they also contribute
significantly to human misery as pathogens (path′-oh-jenz). The vast majority of microorganisms
that associate with humans cause no harm. In fact, they provide many benefits to their human
hosts. Note that a diverse microbial biota living in and on humans is an important part of human
well-being. However, humankind is also plagued by nearly 2,000 different microbes that can
cause various types of disease. Any disease caused by a microorganism is termed an infectious
disease. Many diseases are not caused by microorganisms, but by genetic defects, imbalances in
body systems, exposure to chemicals in the environment, among others. Infectious diseases still
devastate human populations worldwide, despite significant strides in understanding and treating
them. The World Health Organization (WHO) estimates there are a total of 10 billion new
infections across the world every year. Infectious diseases are important common causes of death
in much of humankind, and they still kill a significant percentage of the U.S. population. Table
1.2 depicts the 10 top causes of death per year (by all causes, infectious and noninfectious) in the
United States and worldwide.
One of the most eye-opening discoveries in recent years is that many diseases that used to
be considered noninfectious probably do involve microbial infection. One well-known example
is that of gastric ulcers, now known to be caused by a bacterium called Helicobacter. But there
are more. Diseases as different as multiple sclerosis, obsessive compulsive disorder, coronary
artery disease, and even obesity have been linked to chronic infections with microbes. It seems
that the golden age of microbiological discovery, during which all of the “obvious” diseases
were characterized and cures or preventions were devised for them, should more accurately be
referred to as the first golden age. We’re now discovering the subtler side of microorganisms.
Later in this chapter we will introduce the human microbiome—the microbes that call the human
body home from birth onward. We will see that variations in the microbiome also determine a
person’s tendeAs discussed earlier, two basic cell types appeared during evolutionary history.
The bacteria and archaea, along with eukaryotic cells, differ not only in the complexity of
their cell structure but also in contents and function. In general, bacterial and archaeal cells are
about 10 times smaller than eukaryotic cells, and they lack many of the eukaryotic cell structures
such as organelles. Organelles are small, membranebound structures in the eukaryotic cell that
perform specific functions and include the nucleus, mitochondria, and chloroplasts. Examples of
bacteria, archaea, and eukaryotic microorganisms are covered in more detail in chapter 3 and 4.
All bacteria and archaea are microorganisms, but only some eukaryotes are microorganisms
(figure 1.5). Also, of course, humans are eukaryotes.
Certain small eukaryotes—such as helminths (worms), many of which can be seen with
the naked eye—are also included in the study of infectious diseases because of the way they are
transmitted and the way the body responds to them, though they are not microorganisms. As
stated previously, viruses are not independently living cellular organisms. Instead, they are small
particles that are at a level of complexity somewhere between large molecules and cells. Viruses
are much simpler than cells. Outside their host, they are composed of a small amount of
hereditary material (either DNA or RNA but never both) wrapped up in a protein covering. Some
viruses have an additional layer, a lipid membrane that is exterior to the protein part. Then we
have prions, which are even simpler than viruses. They contain no nucleic acid, only protein, but
act like infectious microorganisms. As discussed earlier, two basic cell types appeared during
evolutionary history.
The bacteria and archaea, along with eukaryotic cells, differ not only in the complexity of
their cell structure but also in contents and function. In general, bacterial and archaeal cells are
about 10 times smaller than eukaryotic cells, and they lack many of the eukaryotic cell structures
such as organelles. Organelles are small, membranebound structures in the eukaryotic cell that
perform specific functions and include the nucleus, mitochondria, and chloroplasts. Examples of
bacteria, archaea, and eukaryotic microorganisms are covered in more detail in chapter 3 and 4.
All bacteria and archaea are microorganisms, but only some eukaryotes are microorganisms
(figure 1.5). Also, of course, humans are eukaryotes.
Certain small eukaryotes—such as helminths (worms), many of which can be seen with
the naked eye—are also included in the study of infectious diseases because of the way they are
transmitted and the way the body responds to them, though they are not microorganisms. As
stated previously, viruses are not independently living cellular organisms. Instead, they are small
particles that are at a level of complexity somewhere between large molecules and cells. Viruses
are much simpler than cells. Outside their host, they are composed of a small amount of
hereditary material (either DNA or RNA but never both) wrapped up in a protein covering. Some
viruses have an additional layer, a lipid membrane that is exterior to the protein part. Then we
have prions, which are even simpler than viruses. They contain no nucleic acid, only protein, but
act like infectious microorganisms.
If not for the extensive interest, curiosity, and devotion of thousands of microbiologists
over the last 300 years, we would know little about the microscopic realm that surrounds us.
Each additional insight, whether large or small, has added to our current knowledge of living
things and processes. And the discoveries continue. Every day brings new surprises and insights
into the microbial world. This section summarizes the prominent discoveries made in the past
300 years. Spontaneous Generation From very earliest history, humans noticed that when certain
foods spoiled, they became inedible or caused illness, and yet other “spoiled” foods did no harm
and even had enhanced flavor. Indeed, several centuries ago, there was already a sense that
diseases such as the Black Plague and smallpox were caused by some sort of transmissible
matter. But the causes of such phenomena were vague and obscure because, frankly, we couldn’t
see anything amiss. Consequently, they remained cloaked in mystery and regarded with
superstition—a trend that led even well-educated scientists to believe in a concept called
spontaneous generation.
This was the belief that invisible vital forces present in matter led to the creation of life.
The belief was continually reinforced as people observed that meat left out in the open soon
“produced” maggots that mushrooms appeared on rotting wood, seemingly out of nowhere, that
rats and mice emerged from piles of litter, and other similar phenomena. Though some of these
early ideas seem quaint and ridiculous in light of modern knowledge, we must remember that, at
the time, mysteries in life were accepted and the scientific method was not widely practiced.
Even after single-celled organisms were discovered during the mid-1600s, the idea of
spontaneous generation continued to exist. Some scientists assumed that microscopic beings
were an early stage in the development of more complex ones.
Over the subsequent 200 years, scientists waged an experimental battle over the two
hypotheses that could explain the origin of simple life forms. Some tenaciously clung to the idea
of abiogenesis (a = “without”; bio = “life”; genesis = “beginning”— “beginning in absence of
life”), which embraced spontaneous generation. On the other side were advocates of biogenesis
(“beginning with life”) saying that living things arise only from others of their same kind. There
were serious advocates on both sides, and each side put forth what appeared on the surface to be
plausible explanations of why its evidence was more correct. Finally in the mid-1800s, the
acclaimed chemist and microbiologist Louis Pasteur entered the arena. He had recently been
studying the roles of microorganisms in the fermentation of beer and wine, and it was clear to
him that these processes were brought about by the activities of microbes introduced into the
beverage from air, fruits, and grains.
The methods he used to discount spontaneous generation were simple yet brilliant. To
demonstrate that air and dust were the source of microbes, Pasteur filled flasks with broth and
shaped their openings into long, swan-neck-shaped tubes (figure 1.6). The flasks’ openings were
freely open to the air but were curved so that gravity would cause any airborne dust particles to
deposit in the lower part of the necks. He heated the flasks to sterilize the broth and then
incubated them. As long as the flask remained intact, the broth remained sterile; but if the neck
was broken off so that dust fell directly down into the container, microbial growth immediately
commenced.
The Role of the Microscope
True awareness of the widespread distribution of microorganisms and some of their
characteristics was finally made possible by the development of the first microscopes. These
devices revealed microbes as discrete entities sharing many of the characteristics of larger,
visible plants and animals. Probably the earliest record of microbes is in the works of
Englishman Robert Hooke. In the 1660s, Hooke studied many different materials, including
household objects, plants, and trees. He described cellular structures for the first time (in tree
bark) and drew sketches of “little structures” that seemed to be alive. Hooke paved the way for
even more exacting observations of microbes by Antonie van Leeuwenhoek (lay′-oo-wun-hook),
a Dutch linen merchant and self-made microbiologist. Leeuwenhoek taught himself to grind
glass lenses to ever-finer specifications so he could see the threads in his fabrics with better
clarity. Eventually, he became interested in things other than thread counts. He took rainwater
from a clay pot, smeared it on his specimen holder, and peered at it through his finest lens. He
found “animals appearing to me ten thousand times less than those which may be perceived in
the water with the naked eye.”
These events marked the beginning of our understanding of microbes and the diseases
they can cause. Discoveries continue at a breakneck pace, however. In fact, the 2000s are being
widely called the Century of Biology, fueled by our new abilities to study genomes and harness
biological processes. To give you a feel for what has happened most recently, table 1.3 provides
a glimpse of some recent discoveries that have had huge impacts on our understanding of
microbiology. The changes to our view of the role of RNAs that you see in table 1.3 highlight a
feature of biology— and all of science—that is perhaps underappreciated. Because we have thick
textbooks containing all kinds of assertions and “facts,” many people think science is an ironclad
collection of facts. Wrong! Science is an ever-evolving collection of new information, gleaned
from observable phenomena and combined with old information to come up with the current
understandings of nature. Some of the hypotheses explaining these observations have been
confirmed so many times over such a long period of time that they are, if not “fact,” very close to
fact.
Many other hypotheses will be altered over and over again as new findings emerge. And
that is the beauty of science. It is important to understand that modern science is conducted
according to a set of widely accepted “rules,” termed the scientific method (figure 1.8).
Researchers form a hypothesis, and then perform experiments or other types of studies that allow
them to either reject or accept the hypothesis. In real life it can also get much more complicated
than that. Note the blue arrows in the figure indicating that the process can stop and revisit earlier
steps. After the results are communicated (last step in the figure), other scientists review and
repeat the studies in order to verify them or bring them into question. This is a process that
distinguishes true research from even the most educated guesses or opinions.
The Beginnings of Medical Microbiology
Early experiments on the sources of microorganisms led to the profound realization that
microbes are everywhere: Not only are air and dust full of them, but the entire surface of the
earth, its waters, and all objects are inhabited by them. This discovery led to immediate
applications in medicine. So you see that the seeds of medical microbiology were sown in the
mid to latter half of the 19th century (the 1800s) with the introduction of the germ theory of
disease and the resulting use of sterile, aseptic, and pure culture techniques
The discovery and detailed description of heat-resistant bacterial endospores by
Ferdinand Cohn, a German botanist, clarified the reason that heat would sometimes fail to
completely eliminate all microorganisms. The modern sense of the word sterile, meaning
completely free of all life forms (including spores) and virus particles, was established from that
point on. The capacity to sterilize objects and materials is an absolutely essential part of
microbiology, medicine, dentistry, and many industries
At the same time that spontaneous generation was being hotly debated, a few physicians
began to suspect that microorganisms could cause not only spoilage and decay but also human
diseases. It occurred to these rugged individualists that even the human body itself was a source
of infection. In 1843, Dr. Oliver Wendell Holmes, an American physician, published an article in
which he observed that mothers who gave birth at home experienced fewer infections than did
mothers who gave birth in the hospital. A few years later, the Hungarian Dr. Ignaz Semmelweis
showed quite clearly that women became infected in the maternity ward after being examined by
physicians coming directly from the autopsy room—without washing their hands.
In the 1860s, the English surgeon Joseph Lister took notice of these observations and was
the first to introduce aseptic (ay-sep′-tik) techniques aimed at reducing microbes in a medical
setting. Lister’s concept of asepsis was much more limited than our modern precautions. It
mainly involved disinfecting the hands and the air with strong antiseptic chemicals, such as
phenol, prior to surgery. It is hard for us to believe, but as recently as the late 1800s surgeons
wore street clothes in the operating room and had little idea that hand washing was important
(figure 1.9). Lister’s techniques and the application of heat for sterilization became the
foundations for microbial control by physical and chemical methods, which are still in use today
All microorganisms—indeed, all organisms—are constructed from just a few major types
of biological molecules, called macromolecules—“macro” because they are often very large.
They include four main families: carbohydrates, lipids, proteins, and nucleic acids (table 1.4). All
macromolecules except lipids are formed by polymerization, a process in which repeating
subunits termed monomers are bound into chains of various lengths termed polymers. For
example, proteins (polymers) are composed of a chain of amino acids (monomers). In the
following section and in later chapters, we consider numerous concepts relating to the roles of
macromolecules in cells. Table 1.5 presents the important structural features of the four main
macromolecules.
Carbohydrates: Sugars and Polysaccharides The term carbohydrate originates from the
composition of members of this class: They are combinations of carbon (carbo-) and water.
Carbohydrates can be generally represented by the formula (CH2O) n, in which n indicates the
number of units of this combination of atoms. Some carbohydrates also contain additional atoms
of sulfur or nitrogen Monosaccharides and disaccharides are specified by combining a prefix that
describes some characteristic of the sugar with the suffix -ose. For example, hexoses are
composed of 6 carbons, and pentoses contain 5 carbons. Glucose (Gr. glyko, “sweet”) is the most
common and universally important hexose; fructose is named for fruit (one place where it is
found); and xylose, a pentose, derives its name from the Greek word for wood. Disaccharides are
named similarly: lactose (L. lacteus, “milk”) is an important component of milk; maltose means
malt sugar; and sucrose (Fr. Sucre, “sugar”) is common table sugar or cane sugar.
The Functions of Polysaccharides contribute to structural support and protection and also
serve as nutrient and energy stores. The cell walls in plants and many microscopic algae derive
their strength and rigidity from cellulose, a long, fibrous polysaccharide. Because of this role,
cellulose is probably one of the most common organic substances on the earth. Interestingly, it is
digestible only by certain bacteria, fungi, and protozoa. These microbes, called decomposers,
play an essential role in breaking down and recycling plant materials. Structural polysaccharides
can be conjugated (chemically bonded) to amino acids, nitrogen bases, lipids, or proteins. Agar,
an indispensable polysaccharide in preparing solid culture media, is a natural component of
certain seaweeds. It is a complex polymer of galactose and sulfur-containing carbohydrates.
The exoskeletons of certain fungi contain chitin (ky′-tun), a polymer of glucosamine (a
sugar with an amino functional group). Peptidoglycan (pep-tih-doh-gly′-kan) is one special class
of compounds in which polysaccharides (glycans) are linked to peptide fragments (a short chain
of amino acids). This molecule provides the main source of structural support to the bacterial cell
wall. The outer covering of gram-negative bacteria also contains lipopolysaccharide, a complex
of lipid and polysaccharide responsible for symptoms such as fever and shock (see chapters 3
and 11). The outer surface of many cells has a “sugar coating” composed of polysaccharides
bound in various ways to proteins (this combination is termed a glycoprotein). This structure,
called the glycocalyx, serves as a protective outer layer, and also can play a role in attachment of
the cells to other cells or surfaces. Small sugar molecules on cell surfaces also account for the
differences in human blood types. Viruses also have glycoproteins on their surface with which
they bind to and invade their host cells.
Lipids: Fats, Phospholipids, Steroids, and Waxes There are four main types of
compounds classified as lipids: triglycerides, phospholipids, steroids, and waxes. The
triglycerides are an important storage lipid. This category includes fats and oils. Triglycerides are
composed of a single molecule of glycerol bound to three fatty acids (figure 1.11). Glycerol is a
3- carbon alcohol with three OH groups, and fatty acids are long-chain hydrocarbon molecules
with a carboxyl group (COOH) at one end that is free to bind to the glycerol. The hydrocarbon
portion of a fatty acid can vary in length from 4 to 24 carbons—and, depending on the fat, it may
be saturated or unsaturated. If all carbons in the chain are single-bonded to 2 other carbons and 2
hydrogens, the fat is saturated. If there is at least one C=C double bond in the chain, it is
unsaturated. The structure of fatty acids is what gives fats and oils (liquid fats) their greasy,
insoluble nature. In general, solid fats (such as butter) are more saturated, and liquid fats (such as
oils) are more unsaturated.
Membrane Lipids Phospholipids in membranes have a hydrophilic (“water-loving”)
region and a hydrophobic (“waterfearing”) region. The hydrophilic region carries a negative
charge due to a phosphate group attached to an alcohol group. The long fatty acid chains are
uncharged and make that portion of the molecule hydrophobic (figure 1.12a). When exposed to
an aqueous solution, the charged heads are attracted to the water phase, and the nonpolar tails are
repelled from the water phase (figure 1.12b). This property causes lipids to naturally form into
single and double layers (bilayers). When two single layers of polar lipids come together to form
a double layer, the outer hydrophilic face of each single layer will orient itself toward the
solution, and the hydrophobic portions will become immersed in the core of the bilayer. This
behavior allows phospholipids to be the main constituent of all cell membranes. Steroids are
complex ringed compounds commonly found in cell membranes and as animal hormones. The
best known of these is the sterol called cholesterol (figure 1.13). (A sterol is a steroid that has an
OH group.) Cholesterol reinforces the structure of the cell membrane in animal cells and in an
unusual group of cell-wall-deficient bacteria called the mycoplasmas. The cell membranes of
fungi also contain a sterol, called ergosterol.
Proteins: Shapers of Life the predominant organic molecules in cells are proteins. To a
large extent, the structure, behavior, and unique qualities of each living thing are a consequence
of the proteins they contain. The building blocks of proteins are amino acids, which exist in 20
different naturally occurring forms (table 1.6). Various combinations of these amino acids
account for the nearly infinite variety of proteins. Various terms are used to denote the nature of
proteins. Peptide usually refers to a molecule composed of short chains of amino acids, such as a
dipeptide (two amino acids), a tripeptide (three), and a tetrapeptide (four). A polypeptide
contains an unspecified number of amino acids but usually has more than 20 and is often a
smaller subunit of a protein. A protein is the largest of this class of compounds and usually
contains a minimum of 50 amino acids. It is common for the term protein to be used to describe
all of these molecules. In chapter 8, we see that protein synthesis is not just a random connection
of amino acids; it is directed by information provided in DNA.
Protein Structure and Diversity the reason that proteins are so varied and specific is that
the way they are folded makes all the difference with respect to their function. A protein has a
natural tendency to assume more complex levels of organization, called the secondary, tertiary,
and quaternary structures (figure 1.14). The primary (1°) structure is the type, number, and order
of amino acids in the chain, which varies extensively from protein to protein. The secondary (2°)
structure arises when various functional groups (called R groups) exposed on the outer surface of
the molecule interact by forming hydrogen bonds. This interaction causes the amino acid chain
to twist into a coiled configuration called the alpha helix (α helix) or to fold into an accordion
pattern called a beta-pleated sheet (β-pleated sheet). Many proteins contain both types of
secondary configurations. Proteins at the secondary level undergo a third degree of torsion called
the tertiary (3°) structure created by additional bonds between functional groups (figure 1.14c).
In proteins with the sulfur-containing amino acid cysteine, further tertiary stability is achieved
through covalent disulfide bonds between sulfur atoms on two different parts of the molecule.
Some complex proteins also participate in a quaternary (4°) structure, in which more than one
polypeptide forms a large, multiunit protein. This is typical of antibodies and some enzymes that
act in cell synthesis.
RNA: Organizers of Protein Synthesis like DNA, RNA consists of a long chain of
nucleotides. However, RNA is usually a single strand, except in some viruses. It contains ribose
sugar instead of deoxyribose and uracil instead of thymine (see table 1.5). Several functional
types of RNA are formed using the DNA template through a process called transcription. Three
major types of RNA are directly used for protein synthesis. Messenger RNA (mRNA) is a copy
of a gene (a single functional part of the DNA) that provides the order and type of amino acids in
a protein; transfer RNA (tRNA) is a carrier that delivers the correct amino acids for protein
assembly; and ribosomal RNA (rRNA) is a major component of ribosomes (described in chapter
3). A fourth type of RNA is the RNA that acts to regulate the genes and gene expression. More
information on these important processes is presented in chapter 8.
ATP: The Energy Molecule of Cells a relative of RNA involved in an entirely different
cell activity is adenosine triphosphate (ATP). ATP is a nucleotide containing adenine, ribose, and
three phosphates rather than just one (figure 1.16). It belongs to a category of high-energy
compounds (also including guanosine triphosphate [GTP]) that gives off energy when the bond
is broken between the second and third (outermost) phosphate. The presence of these high-
energy bonds makes it possible for ATP to release and store energy for cellular chemical
reactions. Breakage of the bond of the terminal phosphate releases energy to do cellular work
and also generates adenosine diphosphate (ADP). ADP can be converted back to ATP when the
third phosphate is restored, thereby serving as an energy depot. Carriers for oxidationreduction
activities (nicotinamide adenine dinucleotide [NAD], for instance) are also derivatives of
nucleotides
Fundamental Characteristics of Cells The bodies of some living things, such as bacteria
and protozoa, consist of only a single cell, whereas those of animals and plants contain trillions
of cells. Regardless of the organism, all cells have a few common characteristics. They tend to be
spherical, polygonal, cubical, or cylindrical; and their protoplasm (internal cell contents) is
encased in a cell or cytoplasmic membrane. They have chromosomes containing DNA, and
ribosomes for protein synthesis, and they are exceedingly complex in function. Aside from these
few similarities, the contents and structure of the three different cell types—bacterial, archaeal,
and eukaryotic—differ significantly. Animals, plants, fungi, and protozoa are all made up of
eukaryotic cells. Such cells contain a number of complex internal parts called organelles that
perform useful functions for the cell involving growth, nutrition, or metabolism. Organelles are
distinct cell components that perform specific functions and are enclosed by membranes.
Organelles also partition the eukaryotic cell into smaller compartments. The most visible
organelle is the nucleus, a roughly ball-shaped mass surrounded by a double membrane that
contains the DNA of the cell. Other organelles include the Golgi apparatus, endoplasmic
reticulum, vacuoles, and mitochondria. Bacterial and archaeal cells may seem to be the cellular
“have nots” because, for the sake of comparison, they are described by what they lack. They
have no nucleus and generally no other organelles. This apparent simplicity is misleading,
however, because the fine structure of these cells is complex. Overall, bacterial and archaeal
cells can engage in nearly every activity that eukaryotic cells can, and many can function in ways
that eukaryotes cannot. Chapters 3 and 4 delve deeply into the properties of bacterial, archaeal,
and eukaryotic cells.
The science of classifying living beings is taxonomy. It originated more than 250 years
ago when Carl von Linné (also known as Linnaeus; 1701–1778), a Swedish botanist, laid down
the basic rules for classification and established taxonomic categories, or taxa (singular, taxon).
Von Linné realized early on that a system for recognizing and defining the properties of living
beings would prevent chaos in scientific studies by providing each organism with a unique name
and an exact “slot” in which to catalog it. This classification would then serve as a means for
future identification of that same organism and permit people working in many biological fields
to know if they were indeed discussing the same organism. The primary concerns of modern
taxonomy are still naming, classifying, and identifying. These three areas are interrelated and
play a vital role in keeping a dynamic inventory of the extensive array of living and extinct
beings. In general, Nomenclature (naming) is the assignment of scientific names to the various
taxonomic categories and to individual organisms. Classification is the orderly arrangement of
organisms into a hierarchy. Identification is the process of discovering and recording the traits of
organisms so that they may be recognized or named and then classified
Classification schemes are organized into several descending ranks, beginning with the
most general all-inclusive taxonomic category and ending with the smallest and most specific
category. This means that all members of the highest category share only one or a few general
characteristics, whereas members of the lowest category are essentially the same kind of
organism—that is, they share the majority of their characteristics. The taxonomic categories from
top to bottom are domain, kingdom, phylum or division, class, order, family, genus, and species.
That means that each kingdom can be subdivided into a series of phyla or divisions, each phylum
is made up of several classes, each class contains several orders, and so on. Because taxonomic
schemes are to some extent artificial, certain groups of organisms may not exactly fit into the
main categories. In such a case, additional taxonomic levels can be imposed above (super) or
below (sub) a tax on, giving us such categories as “superphylum” and “subclass.” Let’s compare
the taxonomic breakdowns of a human and a protozoan (pro-tuh-zoh′-un) to illustrate the fine
points of this system (figure 1.17).
Humans and protozoa are both organisms with nucleated cells (eukaryotes); therefore,
they are in the same domain (Eukarya), but they are in different kingdoms. Humans are
multicellular animals (kingdom Animalia), whereas protozoa are single-cellular organisms that,
together with algae, belong to the kingdom Protista. To emphasize just how broad the category
“kingdom” is, ponder the fact that we humans belong to the same kingdom as jellyfish. Of the
several phyla within this kingdom, humans belong to the phylum Chordata, but even a phylum is
rather all-inclusive, considering that humans share it with other vertebrates as well as with
creatures called sea squirts. The next level, class Mammalia, narrows the field considerably by
grouping only those vertebrates that have hair and suckle their young. Humans belong to the
order Primates, a group that also includes apes, monkeys, and lemurs. Next comes the family
Hominoidea, containing only humans and apes. The final levels are our genus, Homo (all
modern and ancient humans), and our species, sapiens (meaning “wise”). Notice that for the
human as well as the protozoan, the taxonomic categories in descending order become less
inclusive and the individual members more closely related. In this text, we are usually concerned
with only the most general (domain, kingdom, and phylum) and specific (genus, species)
taxonomic levels.
The Origin and Evolution of Microorganisms
As we indicated earlier, taxonomy, the science of classification of biological species, is
used to organize all of the forms of modern and extinct life. In biology today, there are different
methods for deciding on taxonomic categories, but they all rely on the degree of relatedness
among organisms. The scheme that represents the natural relatedness (relation by descent)
between groups of living beings is called their phylogeny (Gr. phylon, “race or class”; L.
genesis, “origin or beginning”). Biologists use phylogenetic relationships to refine the system of
taxonomy.
To understand the natural history of and the relatedness among organisms, we must
understand some fundamentals of the process of evolution. Evolution is an important theme that
underlies all of biology, including the biology of microorganisms. As we said earlier, evolution
states that the hereditary information in living beings changes gradually through time and that
these changes result in various structural and functional changes through many generations. The
process of evolution is selective in that those changes that most favor the survival and
reproduction of a particular organism or group of organisms tend to be retained, whereas those
that are less beneficial to survival tend to be lost. This is not always the case, but it often is.
Charles Darwin called this process natural selection.
Tools of the Laboratory Methods for the Culturing and Microscopic Analysis of
Microorganisms
When you’re trying to study microorganisms, you are confronted by some unique
problems. First, most habitats (such as the soil, or the human mouth) contain microbes in
complex associations, so it is often necessary to separate the species from one another. Second,
to maintain and keep track of such small research subjects, microbiologists usually have to grow
them under artificial (and thus distorting) conditions. A third difficulty in working with microbes
is that they are not visible to the eye. Fourth, microbes are everywhere, and undesirable ones can
be introduced into your experiment, causing misleading results. Hese procedures make it
possible to handle and maintain microorganisms as discrete entities whose detailed biology can
be studied and recorded. Having said that, keep in mind as we move through this chapter: It is
not necessary to grow a microorganism to identify it anymore, though it still remains a very
common method. You will read about noncultivation methods of identifying microbes in chapter
15. Sometimes growing microbes in isolated cultures can tell you very little about how they act
in a mixed-species environment, but being able to isolate them and study them is also valuable,
as long as you keep in mind that it is an unnatural state for them.
To grow, or culture, microorganisms, one introduces a tiny sample (the inoculum) into a
container of nutrient medium (plural, media). The medium provides an environment in which
they multiply. This process is called inoculation. To avoid introducing unwanted microorganisms
to the medium, any instrument used for picking up the sample and transferring it must be sterile.
The inoculated medium is then incubated under appropriate conditions (next step) and the
resulting growth is called a culture. (Note that we use “culture” both as a verb and as a noun.)
Clinical specimens are obtained from body fluids (blood, cerebrospinal fluid, peritoneal fluid),
discharges (sputum, urine, feces), anatomical sites (throat, nose, ear, eye, genital tract), or
diseased tissue (such as an abscess or wound). Then the specimens are inoculated into medium in
order to identify the microorganisms in them. Other samples subject to microbiological analysis
are soil, water, sewage, foods, air, and inanimate objects.
Once a container of medium has been inoculated, it is incubated, which means it is placed
in a temperature-controlled chamber (incubator) to encourage multiplication. Although there are
microbes that can grow at temperatures ranging from freezing to boiling, the usual temperatures
used in laboratories—especially in medical facilities—fall between 20°C and 45°C. Incubators
can also control the content of atmospheric gases such as oxygen and carbon dioxide that may be
required for the growth of certain microbes. During the incubation period (ranging from a day to
several weeks), the microbe multiplies and produces growth that is observable macroscopically.
Microbial growth in a liquid medium materializes as cloudiness, sediment, scum, or color. The
most common manifestation of growth on solid media is the appearance of colonies, especially
with bacteria and fungi.
Some microbes require only a very few simple inorganic compounds for growth; others
need a complex list of specific inorganic and organic compounds. The trick is figuring out which
nutrients are essential for each different type of microorganism to grow in the laboratory. In fact,
although we have well-developed methods of growing very many microbes, most microbes are
non-cultivable because we don’t know what they need in an artificial setting. This chapter
focuses on the types of nonliving media used to grow bacteria and fungi. (We also refer to these
as artificial media.) Protozoa and helminths are often more complex to cultivate in the
laboratory. Viruses will not grow on nonliving media because they absolutely require their host
cells in order to reproduce themselves. For that reason, viruses are grown in cultures of live cells.
Scientists have developed a method to amplify the numbers of prions in the laboratory, but it is
not considered cultivation in the true sense.
Media whose compositions are precisely chemically defined are termed defined (also
known as synthetic). Such media contain pure organic and inorganic compounds that vary little
from one source to another and have a molecular content specified by means of an exact formula.
Defined media may contain nothing more than a few essential compounds such as salts and
amino acids dissolved in water or may be composed of a variety of defined organic and inorganic
chemicals. Such standardized and reproducible media are most useful for research applications
when the exact concentration of components in the media is controlled so that metabolic
processes of the microbe can be precisely monitored. If even one component of a given medium
is not precisely defined, the medium belongs in the complex category. Complex media contain
extracts of animals, plants, or yeasts, including such materials as ground-up cells, tissues, and
secretions. Examples are blood, serum, and meat extracts or infusions. These materials are all
sure to contain a rich supply of nutrients, although the type and amounts will vary from batch to
batch—which is not a problem for many situations. Other possible ingredients are milk, yeast
extract, soybean digests, and peptone. Nutrient broth, blood agar, and MacConkey agar are all
complex media.
Microbiologists have many types of media at their disposal. For that reason, until
recently, microbiologists knew of only a few species of bacteria or fungi that could not be
cultivated artificially. However, newer DNA detection technologies have shown us that there are
many more microbes that we don’t know how to cultivate in the lab than those that we do.
Although we can now study some vital traits of bacteria without actually growing the bacteria,
developing new media is still important for growing the bacteria that we are discovering using
those genomic methods. General-purpose media are those that will allow the growth of as broad
a spectrum of microbes as possible. As a rule, they are of the complex variety. Examples include
nutrient agar and broth, brain-heart infusion, and trypticase soy agar (TSA). An enriched medium
contains complex organic substances such as blood, serum, hemoglobin, or special growth
factors (specific vitamins, amino acids) that certain species must have in order to grow. Bacteria
that require growth factors and complex nutrients are termed fastidious.
Blood agar is made by adding sterile sheep, horse, or rabbit blood to a sterile agar base
(figure 2.4a). It is widely used to grow fastidious streptococci and other pathogens. Disease-
causing Neisseria (one species causes gonorrhea) are grown on either Thayer-Martin medium or
“chocolate” agar, which is a blood agar with added hemin and nicotinamide adenine dinucleotide
(figure 2.4b). Enriched media are also useful in the clinical laboratory to encourage the growth of
pathogens that may be present in very low numbers, such as in urine or blood specimens.
Differential media do not inhibit the growth of any particular microorganisms but are
designed to display visible differences in how they grow. Differentiation shows up as variations
in colony size or color (figure 2.5), in media color changes, or in the formation of gas bubbles
and precipitates. These variations often come from the type of chemicals these media contain and
the ways that microbes react to them. For example, when microbe X metabolizes a certain
substance not used by organism Y, then X will cause a visible change in the medium and Y will
not (figure 2.6). The simplest differential media show just two reaction types, leading to a “yes”
or “no” situation. For example, the medium will cause one type of bacterial colony to change
color, while the other types of bacteria do not.
Some media are sufficiently complex to allow for three or four different reactions.
Importantly, you should know that a single medium can be both selective and differential, owing
to its different ingredients. MacConkey agar, for example, appears in table 2.3 (selective media)
and table 2.4 (differential media) due to its ability to suppress the growth of some organisms
while producing a visual distinction among the ones that do grow. The agar in figure 2.5
illustrates this activity; you just can’t see the colonies that were suppressed. Media that are both
selective and differential allow for microbial isolation and identification to occur at the same
time, which can be very useful in the screening of patient specimens as well as food and water
samples.
A reducing medium contains a substance (sodium thioglycollate or cystine) that absorbs
oxygen or slows the penetration of oxygen in a medium, thus reducing its availability. Reducing
media are important for growing bacteria that don’t require oxygen (termed anaerobic) or for
determining the oxygen requirements of isolates. Carbohydrate fermentation media contain
sugars that can be fermented (converted to acids) and a pH indicator to show this reaction.
Transport media are used to maintain and preserve specimens that have to be held for a
period of time before clinical analysis or to sustain delicate species that die rapidly if not held
under stable conditions. Assay media are used by technologists to test the effectiveness of
antimicrobial drugs (see chapter 10) and by drug manufacturers to assess the effect of
disinfectants, antiseptics, cosmetics, and preservatives on the growth of microorganisms.
Enumeration media are used by industrial and environmental microbiologists to count the
numbers of organisms in milk, water, food, soil, and other samples.
How does one determine (i.e., identify) what sorts of microorganisms have been isolated
in cultures? Generally, their microscopic appearance is of limited value because many bacteria
have similar shapes. The microscope can be useful in differentiating the smaller, simpler
bacterial cells from the larger, more complex eukaryotic cells. Appearance can be useful in
identifying eukaryotic microorganisms to the level of genus or species because of their
distinctive morphological features. Unfortunately, bacteria are generally not identifiable by these
methods because very different species may appear quite similar. For them, we have to include
other techniques, some of which characterize their cellular metabolism. These methods, called
biochemical tests, can determine fundamental chemical characteristics such as nutrient
requirements, products given off during growth, presence of enzymes, and mechanisms for
deriving energy. Their genetic and immunologic characteristics are also used for identification.
In chapter 15, we present more detailed examples of the most current genotypic and
immunologic identification methods.
When we say that microbes are too small to be seen with the unaided eye, what sorts of
dimensions are we talking about? Let’s compare the size of microbes with the larger organisms
of the macroscopic world and on the other hand with the atoms and molecules of the molecular
world (figure 2.10). Whereas the dimensions of macroscopic organisms are usually given in
centimeters (cm) and meters (m), those of microorganisms fall within the range of millimeters
(mm) to micrometers (μm) to nanometers (nm). The very smallest of the microbes are the prions.
Then there are the viruses. They mostly range from 20 nm to about 400 nm, although there are a
few types that can be as big as 800 nm or 1500 nm. (Those viruses are as big as cells.) The
smallest bacteria are around 200 nm, and the largest are as large as 750 μm. Yeasts (a
singlecelled form of fungus) are generally 3–4 μ m., though some can be much larger. Protozoa
are generally around 100–300 μm. It is much easier to get a feel for the relative sizes by looking
at a visual (figure 2.10). Also consult table 2.5 for a reminder of metric measurements and
relative size.
Magnification occurs in two phases. The first lens in this system (the one closest to the
specimen) is the objective lens, and the second (the one closest to the eye) is the ocular lens, or
eyepiece (figure 2.12). The objective lens forms the initial image of the specimen, called the real
image. When this image is projected up through the microscope body to the plane of the
eyepiece, the ocular lens forms a second image, the virtual image. The virtual image is the one
that will be received by the eye and converted to a retinal and visual image. The magnifying
power of the objective lens usually ranges from 4× to 100×, and the power of the ocular lens is
usually 10×.
The oil immersion lens (100× magnification) uses oil to capture some of the light that
would otherwise be lost to scatter (figure 2.14). Reducing this scatter increases resolution. In
practical terms, the oil immersion lens can resolve any cell or cell part as long as it is at least 0.2
μm in diameter, and it can resolve two adjacent objects as long as they are at least 0.2 μm apart
(figure 2.15). In general, organisms that are 0.5 μm or more in diameter are easily seen. This
includes fungi and protozoa, some of their internal structures, and most bacteria. However, a few
bacteria and most viruses are far too small to be resolved by the optical microscope and require
electron microscopy (discussed later in this chapter). In summary, then, the factor that most
limits the clarity of a microscope’s image is its resolving power. Even if a light microscope were
designed to magnify several thousand times, its resolving power could not be increased, and the
image it produced would simply be enlarged and fuzzy.
The third quality of a well-magnified image is its degree of contrast from its
surroundings. The contrast is measured by a quality called the refractive index. Refractive index
refers to the degree of bending that light undergoes as it passes from one medium, such as water
or glass, to another medium, such as bacterial cells. The higher the difference in refractive
indexes (the more bending of light), the sharper the contrast that is registered by the microscope
and the eye. Because too much light can reduce contrast and burn out the image, an adjustable
iris diaphragm on most microscopes controls the amount of light entering the condenser. The
lack of contrast in cell components can be compensated for by using special lenses (the phase-
contrast microscope) and by adding dyes.
Like images on undeveloped photographic film, the unstained cells of a fixed smear are
very difficult to see, no matter how great the magnification or how fine the resolving power of
the microscope. To solve this problem, stains can be added to the fixed smear, either coloring the
objects (microbes) or coloring the background so that the unstained microbes stand out. Staining
is any procedure that applies colored chemicals called dyes to specimens. Dyes give a color to
cells or cell parts by becoming affixed to them through a chemical reaction. Dyes can be
classified as basic (cationic) dyes, which have a positive charge, or acidic (anionic) dyes, which
have a negative charge. Because chemicals of opposite charge are attracted to each other, cell
parts that are negatively charged will attract basic dyes, and those that are positively charged will
attract acidic dyes. Many cells, especially those of bacteria, have numerous negatively charged
acidic substances on their surfaces and thus stain more readily with basic dyes. Acidic dyes, on
the other hand, tend to be repelled by cells, so they are good for negative staining (staining the
background and leaving cells unstained).
The Gram Stain In 1884, Hans Christian Gram discovered a staining technique that could
be used to make bacteria in infectious specimens more visible. His technique consisted of
sequential applications of crystal violet (the primary dye), Gram’s iodine (the mordant), an
alcohol rinse (decolorizer), and a contrasting counterstain. Bacteria that stain purple are called
gram-positive, and those that stain red are called gram-negative. Gram-variable organisms
produce both pinkand purple-staining cells. The different results in the Gram stain are due to
differences in the structure of the cell envelope and how it reacts to the series of reagents applied
to the cells. We will study it in more detail in chapter 3. This century-old staining method
remains a universal basis for bacterial classification and identification. The Gram stain can also
be a practical aid in diagnosing infection and in guiding drug treatment. For example, Gram
staining a fresh sputum or spinal fluid specimen can help pinpoint the possible cause of infection,
and in some cases it is possible to begin drug therapy on the basis of this stain. Even in this day
of elaborate and expensive medical technology, the Gram stain remains an important first tool in
diagnosis.
Other Differential Stains The acid-fast stain, like the Gram stain, is an important
diagnostic stain that distinguishes acid-fast bacteria (pink) from non-acid-fast bacteria (blue). (In
this context fast means “resistant to.”) This stain originated as a specific method to detect
Mycobacterium tuberculosis in specimens. It was determined that these bacterial cells have a
particularly impervious outer wall that holds fast (tightly or tenaciously) to the dye (carbol
fuchsin) even when washed with a solution containing acid or acid alcohol. This stain is used for
other medically important bacteria, fungi, and protozoa. Often it is performed when a
gramvariable result is seen in a specimen. The endospore stain (spore stain) is similar to the acid-
fast method in that a dye is forced by heat into resistant bodies called endospores (their
characteristics and significance are discussed in chapter 3). This stain is designed to distinguish
between endospores and the cells that they come from (so-called vegetative cells). Of
significance in medical microbiology are the grampositive, endospore-forming members of the
genus Bacillus (the cause of anthrax) and Clostridium (the cause of botulism and tetanus)
Bacteria and Archaea
Both non-eukaryotic and eukaryotic microbes are ubiquitous in the world today.
Although both can cause infectious diseases, treating them with drugs requires different types of
approaches. In this chapter and coming chapters, you’ll discover why that is. The evolutionary
history of non-eukaryotic cells extends back almost 4 billion years. The fact that these organisms
have endured for so long in such a variety of habitats can be attributed to a cellular structure and
function that are amazingly versatile and adaptable.
All bacterial cells invariably have a cytoplasmic membrane, cytoplasm, ribosomes, a
cytoskeleton, and one (or a few) chromosome(s). The majority have a cell wall and a surface
coating called a glycocalyx. Specific structures that are found in some but not all bacteria are
flagella, an outer membrane, pili, fimbriae, nanowires/nanotubes, plasmids, inclusions,
endospores, and microcompartments. Most of these structures are observed in archaea as well.
Many bacteria function as independent single-celled, or unicellular, organisms. Each
individual bacterial cell is fully capable of carrying out all necessary life activities, such as
reproduction, metabolism, and nutrient processing, unlike the more specialized cells of a
multicellular organism. On the other hand, sometimes bacteria can act as a group. When bacteria
are close to one another in colonies or in biofilms, they communicate with each other through
chemicals that cause them to behave differently than if they were living singly. More
surprisingly, some bacteria seem to communicate with each other using structures called
nanotubes or nanowires, which are appendages that can be many micrometers long and are used
for transferring electrons or other substances outside the cell onto metals in the environment.
The wires also intertwine with the wires of neighboring bacteria and can be used for
exchanging nutrients. Bacteria come in all shapes and sizes. They also exist in many different
types of groupings. Let’s start with size. Bacterial cells have an average size of about 1 μm.
Cocci have a circumference of 1 μm, and rods may have a length of 2 μm with a width of 1 μm.
But that’s just the average. As with everything in nature, there is a lot of variation. One of the
largest non-eukaryotes yet discovered is a bacterial species living in ocean sediments near the
African country of Namibia. These gigantic cocci are arranged in strands that look like pearls
and contain hundreds of golden sulfur granules. They are called Thiomargarita namibiensis,
which means “sulfur pearl of Namibia” (figure 3.2).
The size of the individual cells ranges from 100 up to 750 μm (0.1 to 0.75 mm), and
many are large enough to see with the naked eye. By way of comparison, if the average
bacterium were the size of a mouse, Thiomargarita would be as large as a blue whale! On the
other end of the spectrum, we have Mycoplasma cells, and the newly discovered ultra-small
bacteria, which are generally 0.15 to 0.30 μm. One of the most important ways to describe
bacteria is by their shape and their arrangement. Table 3.1 summarizes shapes. Getting to know
these now will be a great help for the rest of your studies in this course. We generally say that
there are three major shapes: round, rod-shaped, and spiral. It is somewhat common for cells of a
single species to vary in shape and size. This phenomenon, called pleomorphism, is due to
individual variations in cell wall structure caused by slight genetic or nutritional differences. For
example, although the cells of Corynebacterium diphtheriae are generally considered rod-shaped,
in culture they display variations such as club- shaped, swollen, curved, filamentous, and
coccoid.
Bacterial cells can also be categorized according to arrangement, or style of grouping.
The main factors influencing the arrangement of a particular cell type are its pattern of division
while it is growing and how the cells remain attached afterward. The greatest variety in
arrangement occurs in cocci, which can be single, in pairs (diplococci), in tetrads (groups of
four), in irregular clusters (as in staphylococci and micrococci), or in chains of a few to hundreds
of cells (streptococci). An even more complex grouping is a cubical packet of eight, sixteen, or
more cells called a sarcina (sar′-sih-nah). Because bacteria usually reproduce by splitting in two
(over and over again), if the divided cells remain attached, they lead to these diverse
arrangements. After division, the resultant daughter cells remain attached.
Rods are less varied in arrangement because they divide only in one plane. They occur
either as single cells, as a pair of cells with their ends attached (diplobacilli), or as a chain of
several cells (streptobacilli). A palisades (pal′-ih-saydz) arrangement, typical of the
Corynebacterium species, is formed when the cells of a chain remain partially attached by a
small hinge region at the ends. The cells tend to fold (snap) back upon each other, forming a row
of cells oriented side by side (figure 3.5). Spirilla are occasionally found in short chains, but
spirochetes rarely remain attached after division.
External Structures
The bacterial flagellum (flah-jel′-em), an appendage of truly amazing construction, is
unique in the biological world. The primary function of flagella is to confer motility, or self-
propulsion— that is, the capacity of a cell to swim freely through an aqueous habitat. The
flagellum has three distinct parts: the filament, the hook (sheath), and the basal body (figure 3.6).
The filament, a helical structure composed of proteins, is approximately 20 nm in diameter and
varies from 1 to 70 μm in length. It is inserted into a curved, tubular hook. The hook is anchored
to the cell by the basal body, a stack of rings firmly anchored through the cell wall, to the
cytoplasmic membrane and the outer membrane. This arrangement permits the hook with its
filament to rotate 360°, rather than undulating back and forth like a whip as was once thought.
Although many archaea possess flagella, recent studies have shown that the structure is quite
different than the bacterial flagellum. It is called archaellum by some scientists.
The flagellum is effective in guiding bacteria through the environment primarily because
the system for detecting chemicals is linked to the mechanisms that drive the flagellum. There
are clusters of receptors located in the cytoplasmic membrane that bind specific molecules
coming from the immediate environment. The attachment of sufficient numbers of these
molecules transmits signals to the flagellum and sets it into rotary motion. The actual “fuel” for
the flagellum to turn is a gradient of protons (hydrogen ions) that are generated by the
metabolism of the bacterium and that bind to and detach from parts of the flagellar motor within
the cytoplasmic membrane, causing the filament to rotate. If several flagella are present, they
become aligned and rotate as a group (figure 3.8). As a flagellum rotates counterclockwise, the
cell itself swims in a smooth linear direction toward the stimulus.
This action is called a run. Runs are interrupted at various intervals by tumbles, during
which the flagellum reverses direction and causes the cell to stop and change its course.
Alternation between runs and tumbles generates what is termed a random walk form of motility
in these bacteria. However, in response to a concentration gradient of an attractant molecule, the
bacterium will begin to slow down its tumbles, permitting longer runs and overall progress
toward the stimulus (figure 3.9). The movement now becomes a biased random walk in which
movement is favored (biased) in the direction of the attractant. But what happens when a
flagellated bacterium wants to run away from a toxic environment? In this case, the random walk
then favors movement away from the concentration of repellent molecules. By delaying tumbles,
the bacterium increases the length of its runs, allowing it to redirect itself away from the negative
stimulus.
Specialized Functions of the Glycocalyx
Capsules are formed by many pathogenic bacteria, such as Streptococcus pneumoniae (a
cause of pneumonia, an infection of the lung), Haemophilus influenzae (one cause of
meningitis), and Bacillus anthracis (the cause of anthrax). Encapsulated bacterial cells generally
have greater disease-causing abilities because capsules protect the bacteria against host white
blood cells called phagocytes. Phagocytes are a natural body defense that can engulf and destroy
foreign cells through phagocytosis, thus preventing infection. A capsular coating blocks the
mechanisms that phagocytes use to attach to and engulf bacteria.
By escaping phagocytosis, the bacteria are free to multiply and infect body tissues.
Encapsulated bacteria that mutate to nonencapsulated forms usually lose their ability to cause
disease. Glycocalyces can be important in formation of biofilms (figure 3.14a). The thick, white
plaque that forms on teeth comes in part from the surface slimes produced by certain streptococci
in the oral cavity. This slime protects them from being dislodged from the teeth and provides a
niche for other oral bacteria that, in time, can lead to dental disease. The glycocalyx of some
bacteria is so highly adherent that it has a significant role in the persistent colonization of
nonliving materials such as plastic catheters, intrauterine devices, and metal pacemakers that are
in common medical use (figure 3.14b).
