Chapter Outline

1.1 What Our Ancestors Knew

1.2 A Systematic Approach
1.3 Types of Microorganisms

From boiling thermal hot springs to deep beneath the Antarctic ice,
microorganisms can be found almost everywhere on earth in great
quantities. Microorganisms (or microbes, as they are also called) are
small organisms. Most are so small that they cannot be seen without a
microscope.

Most microorganisms are harmless to humans and, in fact, many are

helpful. They play fundamental roles in ecosystems everywhere on
earth, forming the backbone of many food webs. People use them to
make biofuels, medicines, and even foods. Without microbes, there
would be no bread, cheese, or beer. Our bodies are filled with
microbes, and our skin alone is home to trillions of them. Some of
them we can’t live without; others cause diseases that can make us
sick or even kill us.

Although much more is known today about microbial life than ever
before, the vast majority of this invisible world remains unexplored.
Microbiologists continue to identify new ways that microbes benefit
and threaten humans.
CLINICAL FOCUS

Part 1

Cora, a 41-year-old lawyer and mother of two, has recently been

experiencing severe headaches, a high fever, and a stiff neck. Her
husband, who has accompanied Cora to see a doctor, reports that
Cora also seems confused at times and unusually drowsy. Based on
these symptoms, the doctor suspects that Cora may have meningitis, a
potentially life-threatening infection of the tissue that surrounds the
brain and spinal cord.

Meningitis has several potential causes. It can be brought on by

bacteria, fungi, viruses, or even a reaction to medication or exposure
to heavy metals. Although people with viral meningitis usually heal on
their own, bacterial and fungal meningitis are quite serious and
require treatment.
Cora’s doctor orders a lumbar puncture (spinal tap) to take three
samples of cerebrospinal fluid (CSF) from around the spinal cord
(Figure 1.2). The samples will be sent to laboratories in three different
departments for testing: clinical chemistry, microbiology, and
hematology. The samples will first be visually examined to determine
whether the CSF is abnormally colored or cloudy; then the CSF will
be examined under a microscope to see if it contains a normal number
of red and white blood cells and to check for any abnormal cell types.
In the microbiology lab, the specimen will be centrifuged to
concentrate any cells in a sediment; this sediment will be smeared on
a slide and stained with a Gram stain. Gram staining is a procedure
used to differentiate between two different types of bacteria (gram-
positive and gram-negative).

About 80% of patients with bacterial meningitis will show bacteria in

their CSF with a Gram stain. Cora’s Gram stain did not show any
bacteria, but her doctor decides to prescribe her antibiotics just in
case. Part of the CSF sample will be cultured—put in special dishes to
see if bacteria or fungi will grow. It takes some time for most
microorganisms to reproduce in sufficient quantities to be detected
and analyzed.
What types of microorganisms would be killed by antibiotic
treatment?

(a)A lumbar puncture is used to take a sample of a patient’s

cerebrospinal fluid (CSF) for testing. A needle is inserted
between two vertebrae of the lower back, called the lumbar
region. (b) CSF should be clear, as in this sample. Abnormally
cloudy CSF may indicate an infection but must be tested further
to confirm the presence of microorganisms. (Credit a:
modification of work by Centers for Disease Control and
Prevention; credit b: modification of work by James Heilman)
Most people today, even those who know very little about
microbiology, are familiar with the concept of microbes, or "germs,"
and their role in human health. Schoolchildren learn about bacteria,
viruses, and other microorganisms, and many even view specimens
under a microscope. But a few hundred years ago, before the
invention of the microscope, the existence of many types of microbes
was impossible to prove. By definition, microorganisms, or
microbes, are very small organisms; many types of microbes are too
small to see without a microscope, although some parasites and fungi
are visible to the naked eye.

Humans have been living with—and using—microorganisms for much

longer than they have been able to see them. Historical evidence
suggests that humans have had some notion of microbial life since
prehistoric times and have used that knowledge to develop foods as
well as prevent and treat disease. In this section, we will explore some
of the historical applications of microbiology as well as the early
beginnings of microbiology as a science.

Fermented Foods and Beverages

People across the world have enjoyed fermented foods and beverages
like beer, wine, bread, yogurt, cheese, and pickled vegetables for all
of recorded history. Discoveries from several archaeological sites
suggest that even prehistoric people took advantage of fermentation
to preserve and enhance the taste of food. Archaeologists studying
pottery jars from a Neolithic village in China found that people were
making a fermented beverage from rice, honey, and fruit as early as
7000 BC.³
Production of these foods and beverages requires microbial
fermentation, a process that uses bacteria, mold, or yeast to convert
sugars (carbohydrates) to alcohol, gases, and organic acids (Figure
1.3). While it is likely that people first learned about fermentation by
accident—perhaps by drinking old milk that had curdled or old grape
juice that had fermented—they later learned to harness the power of
fermentation to make products like bread, cheese, and wine.

Figure 1.3 A microscopic view of Saccharomyces cerevisiae, the

yeast responsible for making bread rise (left). Yeast is a
microorganism. Its cells metabolize the carbohydrates in flour
(middle) and produce carbon dioxide, which causes the bread to rise
(right). (Credit middle: modification of work by Janus Sandsgaard;
credit right: modification of work by "MDreibelbis"/Flickr)
Iceman and Evidence of Early Treatments

Prehistoric humans had a very limited understanding of the causes of

disease, and various cultures developed different beliefs and
explanations. While many believed that illness was punishment for
angering the gods or was simply the result of fate, archaeological
evidence suggests that prehistoric people attempted to treat illnesses
and infections. One example of this is Ötzi the Iceman, a 5300-year-
old mummy found frozen in the ice of the Ötztal Alps on the Austrian-
Italian border in 1991. Because Ötzi was so well preserved by the ice,
researchers discovered that he was infected with the eggs of the
parasite Trichuris trichiura, which may have caused him to have
abdominal pain and anemia. Researchers also found evidence of
Borrelia burgdorferi, a bacterium that causes Lyme disease. Some
researchers think Ötzi may have been trying to treat his infections
with the woody fruit of the Fomitopsis betulinus fungus, which was
discovered tied to his belongings. This fungus has both laxative and
antibiotic properties. Ötzi was also covered in tattoos that were made
by cutting incisions into his skin, filling them with herbs, and then
burning the herbs. There is speculation that this may have been
another attempt to treat his health ailments.
Early Notions of Disease, Contagion, and Containment

Several ancient civilizations appear to have had some understanding

that disease could be transmitted by things they could not see. This is
especially evident in historical attempts to contain the spread of
disease. For example, the Bible refers to the practice of quarantining
people with leprosy and other diseases, suggesting that people
understood that diseases could be communicable. Ironically, while
leprosy is communicable, it is also a disease that progresses slowly.
This means that people were likely quarantined after they had already
spread the disease to others.

Clean water and sanitation are among the most important elements of
healthy societies. The earliest examples of urban sanitation systems
are from the ancient Indus Valley Civilization cities of Mohenjo-daro
and Harappa, located in present-day Pakistan. Constructed in 2500
BCE (about 4,500 years ago), the cities had complex networks of
wells, baths, and drainage systems that stored fresh water and
carried waste away. About two thousand years later, people in the
ancient Greek civilization attributed disease to bad air, mal’aria,
which they called “miasmatic odors.” They developed hygiene
practices that built on this idea. In Rome, they built aqueducts, which
brought fresh water into the city, and a giant sewer, the Cloaca
Maxima, which carried waste away and into the river Tiber. Some
researchers believe that this infrastructure and disease prevention in
Ancient Rome.
Figure 1.4

(a) The Cloaca Maxima, or "Greatest Sewer" (shown in red), ran

through ancient Rome. It was an engineering marvel that carried
waste away from the city and into the river Tiber. (b) These ancient
latrines emptied into the Cloaca Maxima.
Even before the invention of the microscope, some doctors,
philosophers, and scientists made great strides in understanding the
invisible forces—what we now know as microbes—that can cause
infection, disease, and death.

The Greek physician Hippocrates (460–370 BC) is considered the

"father of Western medicine". Unlike many of his ancestors and
contemporaries, he dismissed the idea that disease was caused by
supernatural forces. Instead, he posited that diseases had natural
causes from within patients or their environments. Hippocrates and
his heirs are believed to have written the Hippocratic Corpus, a
collection of texts that make up some of the oldest surviving medical
books. Hippocrates is also often credited as the author of the
Hippocratic Oath, taken by new physicians to pledge their dedication
to diagnosing and treating patients without causing harm.
While Hippocrates is considered the father of Western medicine, the
Greek philosopher and historian Thucydides (460–395 BC) is
considered the father of scientific history because he advocated for
evidence-based analysis of cause-and-effect reasoning. Among his
most important contributions are his observations regarding the
Athenian plague, which killed one-third of the population of Athens
between 430 and 410 BC. Having survived the epidemic himself,
Thucydides made the important observation that survivors did not get
re-infected with the disease, even when taking care of actively sick
people. This observation shows an early understanding of the concept
of immunity.
Marcus Terentius Varro (116–27 BC) was a prolific Roman writer who
was one of the first people to propose the concept that things we
cannot see (what we now call microorganisms) can cause disease. In
Res Rusticae (On Farming), published in 36 BC, he said that
"precautions must also be taken in neighborhood swamps

... because certain minute creatures (animalia minuta) grow there

which cannot be seen by the eye, which float in the air and enter the
body through the mouth and nose and there cause serious diseases."

Centuries later, Islamic scholars, mainly in Persia, built on the

knowledge from Hippocrates as well as from Chinese and Indian
medicine. Foremost among them was Abū Bakr al-Rāzī, usually
referred to as al-Razi or by his Latinized name, Rhazes. He developed
a range of experimental methods to test various aspects of medicine.
For example, to select a location for a hospital, al-Razi hung raw meat
around the city and located the facility in the place where the meat
took the longest to rot. He also was the first to distinguish measles
and smallpox, and undertook experiments to determine which
available treatments were most effective for [Link] al-Razi did
not have the technology to understand the role of microbes, his efforts
to identify the causes of illnesses, rather than solely focusing on the
symptoms, were highly influential.

Islamic physicians created one of the most important medical texts in

history, the Canon of Medicine (Arabic: al-Qānūn fī al-Tibb). Compiled
in 1025 by physician and philosopher Ibn Sina (often referred to as
Avicenna), the encyclopedia included detailed descriptions of the
parts of the body, a detailed account of over 800 medicinal
substances, and pathologies of several illnesses organized by body
part or health event. In the work, Ibn Sina described mechanisms of
contagion, indicated that organisms could be infected by foreign
substances, and that illness could be transmitted by breath. He is also
credited with advancing the practice of isolating people who are sick,
laying the foundation for historical and contemporary quarantine
methods. The Canon was translated into many languages and was a
primary resource for teaching medicine around the world, through the
Renaissance and beyond.

Figure 1.5 (a) Hippocrates, the “father of Western medicine,”

believed that diseases had natural, not supernatural, causes. (b)
Thucydides, the historian, observed that survivors of the Athenian
plague were subsequently immune to the infection. (c) Marcus
Terentius Varro proposed that disease could be caused by "certain
minute creatures... which cannot be seen by the eye." (Credit for
image (c): modification of work by Alessandro Antonelli)
The Birth of Microbiology

While the ancients may have suspected the existence of invisible

“minute creatures,” it wasn’t until the invention of the microscope
that their existence was definitively confirmed. While it is unclear who
exactly invented the microscope, a Dutch cloth merchant named
Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens
powerful enough to view microbes. In 1675, using a simple but
powerful microscope, Leeuwenhoek was able to observe single-celled
organisms, which he described as “animalcules” or “wee little
beasties,” swimming in a drop of rainwater. From his drawings of
these little organisms, we now know he was looking at bacteria and
protists. (We will explore Leeuwenhoek’s contributions to microscopy
further in How We See the Invisible World.)

Nearly 200 years after van Leeuwenhoek got his first glimpse of
microbes, the “Golden Age of Microbiology” spawned a host of new
discoveries between 1857 and 1914. Two famous microbiologists,
Louis Pasteur and Robert Koch, were especially active in advancing
our understanding of the unseen world of microbes (Figure 1.6).
Pasteur, a French chemist, showed that individual microbial strains
had unique properties and demonstrated that fermentation is caused
by microorganisms. He also invented pasteurization, a process used to
kill microorganisms responsible for spoilage, and developed vaccines
for the treatment of diseases, including rabies, in animals and
humans. Koch, a German physician, was the first to demonstrate the
connection between a single, isolated microbe and a known human
disease. For example, he discovered the bacteria that cause anthrax
(Bacillus anthracis), cholera (Vibrio cholerae), and tuberculosis
(Mycobacterium tuberculosis).

We will discuss these famous microbiologists, and others, in later

chapters.
MICRO CONNECTIONS

Microbiology Toolbox

Because individual microbes are generally too small to be seen with

the naked eye, the science of microbiology is dependent on
technology that can artificially enhance the capacity of our natural
senses of perception. Early microbiologists like Pasteur and Koch had
fewer tools at their disposal than are found in modern laboratories,
making their discoveries and innovations that much more impressive.
Later chapters of this text will explore many applications of
technology in depth, but for now, here is a brief overview of some of
the fundamental tools of the microbiology lab.
 Microscopes produce magnified images of microorganisms,
human cells and tissues, and many other types of specimens too
small to be observed with the naked eye.
 Stains and dyes are used to add color to microbes so they can
be better observed under a microscope. Some dyes can be used
on living microbes, whereas others require that the specimens
be fixed with chemicals or heat before staining. Some stains only
work on certain types of microbes because of differences in their
cellular chemical composition.
 Growth media are used to grow microorganisms in a lab
setting. Some media are liquids; others are more solid or gel-
like. A growth medium provides nutrients, including water,
various salts, a source of carbon (like glucose), and a source of
nitrogen and amino acids (like yeast extract) so microorganisms
can grow and reproduce. Ingredients in a growth medium can be
modified to grow unique types of microorganisms.
 A Petri dish is a flat-lidded dish that is typically 10–11 centimeters
(cm) in diameter and 1–1.5 cm high. Petri dishes made out of either
plastic or glass are used to hold growth media.

 Test tubes are cylindrical plastic or glass tubes with rounded

bottoms and open tops. They can be used to grow microbes in broth,
or semisolid or solid growth media.

 A Bunsen burner is a metal apparatus that creates a flame that

can be used to sterilize pieces of equipment. A rubber tube carries
gas (fuel) to the burner. In many labs, Bunsen burners are being
phased out in favor of infrared microincinerators, which serve a
similar purpose without the safety risks of an open flame.

 An inoculation loop is a handheld tool that ends in a small wire

loop. The loop can be used to streak microorganisms on agar in a
Petri dish or to transfer them from one test tube to another. Before
each use, the inoculation loop must be sterilized so cultures do not
become contaminated.
The Science of Taxonomy

Taxonomy is the classification, description, identification, and

naming of living organisms. Classification is the practice of organizing
organisms into different groups based on their shared characteristics.
The most famous early taxonomist was a Swedish botanist, zoologist,
and physician named Carolus Linnaeus (1701–1778). In 1735,
Linnaeus published Systema Naturae, an 11-page booklet in which he
proposed the Linnaean taxonomy, a system of categorizing and
naming organisms using a standard format so scientists could discuss
organisms using consistent terminology. He continued to revise and
add to the book, which grew into multiple volumes (Figure 1.8).
In his taxonomy, Linnaeus divided the natural world into three
kingdoms: animal, plant, and mineral (the mineral kingdom was later
abandoned). Within the animal and plant kingdoms, he grouped
organisms using a hierarchy of increasingly specific levels and
sublevels based on their similarities. The names of the levels in
Linnaeus’s original taxonomy were kingdom, class, order, family,
genus (plural: genera), and species. Species was, and continues to be,
the most specific and basic taxonomic unit.
Evolving Trees of Life (Phylogenies)

With advances in technology, other scientists gradually made

refinements to the Linnaean system and eventually created new
systems for classifying organisms. In the 1800s, there was a growing
interest in developing taxonomies that took into account the
evolutionary relationships, or phylogenies, of all different species of
organisms on earth. One way to depict these relationships is via a
diagram called a phylogenetic tree (or tree of life). In these diagrams,
groups of organisms are arranged by how closely related they are
thought to be. In early phylogenetic trees, the relatedness of
organisms was inferred by their visible similarities, such as the
presence or absence of hair or the number of limbs. Now, the analysis
is more complicated. Today, phylogenetic analyses include genetic,
biochemical, and embryological comparisons, as will be discussed
later in this chapter.

Linnaeus’s tree of life contained just two main branches for all living
things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a
German biologist, philosopher, and physician, proposed another
kingdom, Protista, for unicellular organisms (Figure 1.9). He later
proposed a fourth kingdom, Monera, for unicellular organisms whose
cells lack nuclei, like bacteria.

Nearly 100 years later, in 1969, American ecologist Robert Whittaker

(1920–1980) proposed adding another kingdom—Fungi—in his tree of
life. Whittaker’s tree also contained a level of categorization above the
kingdom level—the empire or superkingdom level—to distinguish
between organisms that have membrane-bound nuclei in their cells
(eukaryotes) and those that do not (prokaryotes).Empire Prokaryota
contained just the Kingdom Monera. The Empire Eukaryota contained
the other four kingdoms: Fungi, Protista, Plantae, and Animalia.
Whittaker’s five-kingdom tree was considered the standard phylogeny
for many years.

Figure 1.10 shows how the tree of life has changed over time. Note
that viruses are not found in any of these trees. That is because they
are not made up of cells and thus it is difficult to determine where
they would fit into a tree of life.
CILINICAL FOCUS
Part 2

Antibiotic drugs are specifically designed to kill or inhibit the growth

of bacteria. But after a couple of days on antibiotics, Cora shows no
signs of improvement. Also, her CSF cultures came back from the lab
negative. Since bacteria or fungi were not isolated from Cora’s CSF
sample, her doctor rules out bacterial and fungal meningitis. Viral
meningitis is still a possibility.

However, Cora now reports some troubling new symptoms. She is

starting to have difficulty walking. Her muscle stiffness has spread
from her neck to the rest of her body, and her limbs sometimes jerk
involuntarily. In addition, Cora’s cognitive symptoms are worsening.
At this point, Cora’s doctor becomes very concerned and orders more
tests on the CSF samples.
The Role of Genetics in Modern Taxonomy
Haeckel’s and Whittaker’s trees presented hypotheses about the
phylogeny of different organisms based on readily observable
characteristics. But the advent of molecular genetics in the late 20th
century revealed other ways to organize phylogenetic trees. Genetic
methods allow for a standardized way to compare all living organisms
without relying on observable characteristics that can often be
subjective. Modern taxonomy relies heavily on comparing the nucleic
acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or
proteins from different organisms. The more similar the nucleic acids
and proteins are between two organisms, the more closely related
they are considered to be.
In the 1970s, American microbiologist Carl Woese discovered what
appeared to be a “living record” of the evolution of organisms. He and
his collaborator George Fox created a genetics-based tree of life
based on similarities and differences they observed in the gene
sequences coding for small subunit ribosomal RNA (rRNA) of different
organisms. In the process, they discovered that a certain type of
bacteria, called archaebacteria (now known simply as archaea), were
significantly different from other bacteria and eukaryotes in terms of
their small subunit rRNA gene sequences. To accommodate this
difference, they created a tree with three Domains above the level of
Kingdom: Archaea, Bacteria, and Eukarya (Figure 1.11). Analysis of
small subunit rRNA gene sequences suggests archaea, bacteria, and
eukaryotes all evolved from a common ancestral cell type. The tree is
skewed to show a closer evolutionary relationship between Archaea
and Eukarya than they have to Bacteria.
Scientists continue to use analysis of RNA, DNA, and proteins to
determine how organisms are related. One interesting, and
complicating, discovery is that of horizontal gene transfer—when a
gene of one species is absorbed into another organism’s genome.
Horizontal gene transfer is especially common in microorganisms and
can make it difficult to determine how organisms are evolutionarily
related. Consequently, some scientists now think in terms of “webs of
life” rather than “trees of life.”
Naming Microbes

In developing his taxonomy, Linnaeus used a system of binomial

nomenclature, a two-word naming system for identifying organisms
by genus and specific epithet. For example, modern humans are in the
genus Homo and have the specific epithet name sapiens, so their
scientific name in binomial nomenclature is Homo sapiens. In
binomial nomenclature, the genus part of the name is always
capitalized; it is followed by the specific epithet name, which is not
capitalized. Both names are italicized. When referring to the species
of humans, the binomial nomenclature would be Homo sapiens.
Taxonomic names in the 18th through 20th centuries were typically
derived from Latin, since that was the common language used by
scientists when taxonomic systems were first created. Today, newly
discovered organisms can be given names derived from Latin, Greek,
or English. Sometimes these names reflect some distinctive trait of
the organism; in other cases, microorganisms are named after the
scientists who discovered them. The archaeon Haloquadratum
walsbyi is an example of both of these naming schemes. The
genus, Haloquadratum, describes the microorganism’s saltwater
habitat (halo is derived from the Greek word for “salt”) as well as the
arrangement of its square cells, which are arranged in square clusters
of four cells (quadratum is Latin for “foursquare”). The
species, walsbyi, is named after Anthony Edward Walsby, the
microbiologist who discovered Haloquadratum walsbyi in 1980. While
it might seem easier to give an organism a common descriptive name
—like a red-headed woodpecker—we can imagine how that could
become problematic. What happens when another species of
woodpecker with red head coloring is discovered? The systematic
nomenclature scientists use eliminates this potential problem by
assigning each organism a single, unique two-word name that is
recognized by scientists all over the world.

Same Name, Different Strain

Within one species of microorganism, there can be several subtypes

called strains. While different strains may be nearly identical
genetically, they can have very different attributes. The bacterium
Escherichia coli is infamous for causing food poisoning and travelers
diarrhea. However, there are actually many different strains of E. coli,
and they vary in their ability to cause disease.

One pathogenic (disease causing) E. coli strain that you may have
heard of is E. coli O157:H7 . In humans, infection from E. coli
O157:H7 can cause abdominal cramps and diarrhea. Infection usually
originates from contaminated water or food, particularly raw
vegetables and undercooked meat. In the 1990s, there were several
large outbreaks of E. coli O157:H7 thought to have originated in
undercooked hamburgers.

While E. coli O157:H7 and some other strains have given E. coli a bad
name, most E. coli strains do not cause disease. In fact, some can be
helpful. Different strains of E. coli found naturally in our gut help its
digest our food, provide us with some needed chemicals, and fight
against pathogenic microbes.

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.
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 (Figure 1.14). 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

Protists are an informal grouping of eukaryotes that are not plants,

animals, or fungi. Some algae are protists and others are bacteria; all
protozoa are examples of protists.

Algae (singular: algal) are mostly made up of protists that can be

either unicellular or multicellular and vary widely in size, appearance,
and habitat (Figure 1.15). Algal protists 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. Ovarobacteria, a type of
bacteria, is also considered an algae, but these organisms are
bacterial prokaryotes and therefore have a peptidoglycan-based cell
wall, unlike the cellulose-based cell wall of the algal protists. Because
other organisms can use the waste products of all algae 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 (Figure 1.16).
Jungi

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 (Figure 1.17).
MICROBIOLOGY AS A FIELD OF STUDY

Microbiology is a broad term that encompasses the study of all

different types of microorganisms. But in practice, microbiologists
tend to specialize in one of several subfields. For
example, bacteriology is the study of bacteria; mycology is the study
of fungi; protozoology is the study of protozoa; parasitology is the
study of helminths and other parasites; and virology is the study of
viruses (Figure 1.21).
Immunology, the study of the immune system, is often included in the
study of microbiology because host-pathogen interactions are central
to our understanding of infectious disease processes. Microbiologists
can also specialize in certain areas of microbiology, such as clinical
microbiology, environmental microbiology, applied microbiology, or
food microbiology.

In this textbook, we are primarily concerned with clinical applications

of microbiology, but since the various subfields of microbiology are
highly interrelated, we will often discuss applications that are not
strictly clinical.