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 Prescot’s
Microbiology
Tenth Edition

Willey Sherwood Woolverton

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A Modern Approach to Microbiology

Evolution as a Framework Brief Contents

Introduced immediately in chapter 1 and used as an overarching
theme throughout, evolution helps unite microbiological con-
cepts and provides a framework upon which students can build
About the Authors iv 24 Actinobacteria: The High G 1 C Gram-Positive
Preface v Bacteria 552
25 Protists 563
their knowledge. Part One Introduction to Microbiology
26 Fungi (Eumycota) 583
27 Viruses 597
1 The Evolution of Microorganisms and Microbiology 1
2 Microscopy 22
Part Six Ecology and Symbiosis
3 Bacterial Cell Structure 42
28 Biogeochemical Cycling and Global Climate
4 Archaeal Cell Structure 80
Change 623

An Introduction to the Entire Microbial World

5 Eukaryotic Cell Structure 90
29 Methods in Microbial Ecology 637
6 Viruses and Other Acellular Infectious Agents 109
30 Microorganisms in Marine and Freshwater
Ecosystems 650

Covered in chapters 3–6, the separate chapters on the structure Part Two Microbial Nutrition, Growth, and Control 31 Microorganisms in Terrestrial Ecosystems 667
32 Microbial Interactions 685
and function of bacteria and archaea are followed by the discus-
7 Microbial Growth 132
8 Control of Microorganisms in the Environment 172
Part Seven Pathogenicity and Host Response
sion of eukaryotic cells preceding viruses.
9 Antimicrobial Chemotherapy 188
33 Innate Host Resistance 707
34 Adaptive Immunity 736
Part Three Microbial Metabolism 35 Pathogenicity and Infection 770
10 Introduction to Metabolism 208
11 Catabolism: Energy Release and Conservation 227 Part Eight Microbial Diseases, Detection, and
12 Anabolism: The Use of Energy in Biosynthesis 262 Their Control

Broad Coverage of Microbial Ecology Part Four Microbial Molecular Biology and Genetics
36 Clinical Microbiology and Immunology 786
37 Epidemiology and Public Health Microbiology 806

The importance and multidisciplinary nature of microbial ecology 13 Bacterial Genome Replication and Expression 284 38 Human Diseases Caused by Viruses and Prions 827
14 Regulation of Bacterial Cellular Processes 332 39 Human Diseases Caused by Bacteria 859

is demonstrated by content that ranges from global climate 15 Eukaryotic and Archaeal Genome Replication and 40 Human Diseases Caused by Fungi and Protists 902
Expression 349

change to the human microbiome. 16 Mechanisms of Genetic Variation 369

17 Recombinant DNA Technology 400
Part Nine Applied Microbiology
41 Microbiology of Food 927
18 Microbial Genomics 419 42 Biotechnology and Industrial Microbiology 947
43 Applied Environmental Microbiology 964

Part Five The Diversity of the Microbial World Appendix 1 A Review of the Chemistry of
Biological Molecules A-1
19 Microbial Taxonomy and the Evolution of Diversity 443
20 Archaea 464 Appendix 2 Common Metabolic Pathways A-9
728 CHAPTER 33 | Innate Host Resistance
21 Deinococci, Mollicutes, and Nonproteobacterial Appendix 3 Microorganism Pronunciation Guide A-17
Gram-Negative Bacteria 483 Glossary G-1
22 Proteobacteria 504 Credits C-1
Figure 33.17 Recognition of
Microbe-Associated Molecular 23 Firmicutes: The Low G 1 C Gram-Positive Bacteria 539 Index I-1
Patterns (MAMPs) by Pattern
Recognition Molecules (PRMs). iii
MAMPs bind PRMs, especially
IA

LAM
ER

toll-like receptors (TLRs), C-type RIA

TE
CT

C
lectin receptors (CLRs), and other BA
BA

PGN

Molecular Microbiology and Immunology

pattern recognition receptors.
LPS BLP wiL81590_fm_i-xxii.indd 3 29/09/15 1:31 PM
PRM binding results in signaling
that upregulates cytokine gene LTA Zymosan
expression through common signal
transduction pathways, like NFkB.
Flagellin The tenth edition includes updates on genetics, biotechnology,
MD2
genomics and metagenomics, and immunology. The discus-
CD14
sion of eukaryotic and archaeal genetics has been expanded,
CD1
4
strengthening our understanding of the relatedness of genetic
TLR6
TLR2
TLR2

TLR5

10
TLR1

information flow observed in these organisms. A streamlined

TLR
TLR4
TLR4

discussion of immunity, with enhanced detail between innate

and adaptive linkages, helps students grasp the complexity and
MyD88
specificity of immune responses.
9
DNA CpG TLR

Kinase
Cascades
TRIF
ENDOSOME

Viral
dsRNA
R3
TL
TLR8
TLR7

CYTOPLASM

NUCLEUS

NFkB

wiL81590_ch33_707-735.indd 728 9/3/15 2:34 PM

viii
 A Modern Approach to Microbiology

694 CHAPTER 32 | Microbial Interactions

thermautotrophicus. Remarkably, the flagellar tip protein FliD
serves as an interspecies signal to increase the rate of methanogen-
esis by M. thermautotrophicus. Methanogens and methano-
trophs (section 20.4)
Retrieve, Infer, Apply
1. How could one test to see if an insect-microbe relationship is
mutualistic?
2. What is the role of the Riftia tube worm’s hemoglobin in the success
of the tube worm–endosymbiont mutualistic relationship?
3. How is the Riftia tube worm endosymbiont similar to cyanobacteria?
21st-Century Microbiology
Prescott’s Microbiology leads the way with text devoted to global
So far all our examples have featured symbionts that promote
the growth of hosts in exchange for a safe, nutrient-rich home. The
example of the Gram-negative bacterium Xenorhabdus nematoph-
climate change, biofuels, and microbial fuel cells. For more, see
chapters 28, 30, 42, and 43.
ila and its nematode (worm) host Steinernema carpocapsae is re-
markable because the bacterium contributes directly to the
reproductive success of its host. Juvenile nematodes harboring X.
nematophila within their guts live in the soil. In order to mature, the
juvenile nematode must find an insect to infect and consume; this is
when things get really interesting (figure 32.8). As the hungry juve-
nile nematode consumes insect blood (haemolymph), X. nematoph-
ila is excreted in nematode feces. These are now free-living X.
nematophila and as these bacteria replicate, they secrete chemicals

Metagenomics and the Human Microbiome

How is it different?
that kill the already miserable insect. Once the insect is dead, the
4. What is meant by “tight trophic coupling” between the coral animal
bacteria switch to the production of different compounds that protect
and its microbial symbionts?
the insect from degradation by other bacteria and from attack by
5. Why is it important that the rumen is a reducing environment?
ants, thereby protecting the home of their host nematode. Amaz-
6. Describe the mutualism between methanogenic archaea and their
ruminant hosts and between methanogens and bacteria such as
Syntrophobacter spp.
ingly, as the process continues, X. nematophila produces yet a differ-
ent set of molecular signals that trigger S. carpocapsae development
The importance of metagenomics in understanding the role of
microbes in all environments and in exploring symbionts of in-
to adulthood. A single insect cadaver may host many adult nema-
todes that mate, yielding a cadaver that ultimately teems with S.
Cooperation: Nonobligatory Positive Interactions carpocapsae eggs. As these eggs mature to the juvenile stage with
Between Host and Microbe
For most microbial ecologists, the nonobligatory aspect between
X. nematophila symbionts, they leave to find new insect homes and
start the cycle anew. Because the partners can be grown separately vertebrates and humans is threaded throughout the text. Special
host and symbiont differentiates cooperation from mutualism in the laboratory, it has been possible to dissect these events at the
(figure 32.1). Unfortunately, it is often difficult to distinguish
obligatory from nonobligatory because that which is obligatory
structural, molecular, and biochemical level, making this an impor-
tant model system.
emphasis on the power of metagenomics is found in chapters 1,
in one habitat may not be in another (e.g., the laboratory). None-
theless, the most useful distinction between cooperation and mu-
tualism is the observation that cooperating organisms can grow
Certainly the most provocative cooperative associations to
receive recent attention are those between the human host and our
gut microbiota. Although the typical human gut hosts 500 to 1,000
18, 28, 32, and 42.
independently, although they may not function as well. different microbial species
(most of which have not been
1 X. nematophila live in juvenile
cultured), the Gram-negative
S. carpocapsae gut but is not
shed because nematode does not bacterium Akkermansia mu-
feed at this stage ciniphila is particularly inter-
esting. This microorganism is
Nematode uses insect
corpse as nutrient source
to reproduce;
5
2
critical to maintaining the
mucosal barrier that separates
microbes within the gut and
Laboratory Safety
X. nematophila colonizes the underlying, sterile struc-
Reflecting recommendations from the Centers for Disease Con-
S. carpocapsae
juveniles before they emerge
infects an insect, often tures. It accomplishes this in
in the butterfly family several ways, including the
X. nematophila -
S. carpocapsae Cooperative
Symbiosis
stimulation of host mucus and
antimicrobial peptide pro-
duction and promoting tight
trol and Prevention, along with the American Society for
junction formation between
epithelial cells. This is impor-
­Microbiology, chapter 37 provides specific guidance for labora-
tory best practices to help instructors provide safe conditions
tant because recent evidence
suggests that the lipopolysac-
4 3 charide from Gram-negative
X. nematophila produces
antimicrobial compounds As the nematode starts
gut bacteria that enters the
host’s bloodstream contrib- during the teaching of laboratory exercises.
preventing other microorganisms feeding, X. nematophila released utes a state of sustained in- 26.6 Basidiomycota Includes Mushrooms and Plant Pathogens 593
from consuming the insect cadaver and produces molecules that kill flammation, called metabolic
the insect endotoxemia. This has been
Figure 32.8 The Xenorhabdus nematophila - Steinernema carpocapsae Is an Intriguing Model Bacterial-Nematode linked to conditions such as
System. obesity, type 2 diabetes, and

DISEASE
wiL81590_ch32_685-706.indd 694
26.1 White-Nose Syndrome Is Decimating North American Bat Populations
9/30/15 6:48 PM

Special Interest Essays Bats evoke all kinds of images. Some people immediately
think of vampire bats and are repulsed. Others think of large
wings, muzzle, and ears where it erodes the epidermis before
invading the underlying skin and connective tissue. Despite the
fruit bats often called flying foxes. If you have spent a sum- name WNS, the primary site of infection (and the anatomical
Organized into four themes—Microbial Diversity & Ecology, mer evening outdoors on the east coast of North America, site harmed most) is the wing. Wings provide a large surface
mosquitoes and the small bats that eat them may come to area for colonization, and once infected, the thin layer of skin
Techniques & Applications, Historical Highlights, and Disease— mind. A new scene can now be added to these: bats with white is easily damaged, leading to adverse physiological changes
fungal hyphae growing around their muzzles (box figure). during hibernation. These in turn result in premature awaken-
these focused and interesting essays provide additional insight to This is the hallmark of white-nose syndrome (WNS), and if ing, loss of essential fat reserves, and strange behavior.
its rate of infection continues unchecked, it is projected to Where did this pathogen come from and why does it
relevant topics. eliminate the most common bat species in eastern North infect bats? The best hypothesis regarding its origin is that
America (Myotis lucifugus) by 2026. humans inadvertently brought it from Europe, where it
4.4 Many Archaea Have External Structures Used for Attachment and Motility 87
WNS was first spotted in 2006 among bats hibernating causes mild infection in at least one hibernating bat species.
in a cave near Albany, NY. Scientists quickly became alarmed This makes P. destructans an apparent case of pathogen
for two reasons. First, it spreads rapidly—it’s known to occur pollution—the human introduction of invasive pathogens of
in at least 11 bat species and is now found in 25 states in the wildlife and domestic animal populations that threaten biodi-
MICROBIAL DIVERSITY & ECOLOGY United States and three Canadian provinces. Second, it is
deadly. The population of bats declines from 30 to 99% in any
versity and ecosystem function.
The capacity of P. destructans to sweep through bat pop-
given infected hibernacula (the place where bats hibernate, ulations results from a “perfect storm” of host- and pathogen-
4.1 What’s in a Name? which unfortunately rhymes with Dracula). associated factors. P. destructans is psychrophilic, with a
WNS is caused by the ascomycete Pseudogymnoascus de- growth optimum around 128C; it does not grow above 208C.
Each day soon-to-be parents around the world agonize over long cilia. Despite this, use of the term “flagella” when refer-
structans (formerly Geomyces destructans). It colonizes a bat’s All infected bat species hibernate in cold and humid environ-
what to name their babies. Is the name too popular or too ring to long cilia persisted. When bacterial flagella were
ments such as caves and mines. Because their metabolic rate
unusual? Will it lead to undesirable nicknames? Was it the discovered, they too were named flagella. Eventually their
is drastically reduced during hibernation, their body tempera-
name of an unsavory historical figure? Though scientists ultrastructure and function were discovered and shown to be
probably don’t agonize over what to call new organisms, distinct. As we describe in chapter 3, their structure is much ture reaches that of their surroundings, between 2 and 78C.
cellular structures, or other natural phenomena, they do try simpler, with the helical filament composed of a single type Thus WNS is only seen in hibernating bats or those that have
to choose names carefully. Often the names have Greek or of protein. It propels the cell by rotating. just emerged from hibernation. When metabolically active,
Latin roots that provide some information about the object With this knowledge, scientists began debating new the bat’s body temperature is too warm to support pathogen
being named. For instance, the archaeon Pyrococcus names for these structures. One suggestion was to reserve growth.
furiosus, a name that means rushing fireball, was so named the term flagella for the bacterial organelle and to change While it is too late to save the estimated 6 million bats
because it is spherical, moves rapidly, and loves heat. Sci- the name of eukaryotic flagella to undilapodia, which that have already succumbed to WNS, microbiologists, con-
entists also take care in naming things so that the names essentially means “waving feet.” Undilapodia did not gain servationists, and government agencies are trying to limit the
don’t lead to misconceptions. Unfortunately, sometimes acceptance and finally scientists decided to use the term continued decline in bat populations. Caves have been closed
scientists get it wrong, and new names are suggested. Sug- cilia for both cilia and flagella. More recently, studies of to human traffic, and protocols for decontamination after vis-
gesting new names can lead to considerable debate and archaeal flagella led to the discovery that these are very dif- iting hibernacula have been developed to limit the spread
confusion about which terminology to use. Such is the case ferent from bacterial flagella and eukaryotic cilia, and a from cave to cave. Although we cannot cure sick bats, it is our
with the term flagella. new debate has begun. Over the last few years some scien- responsibility to stop the continued spread of this pathogen.
For decades, long, hairlike structures have been called tists have suggested that three different terms be used:
Geomyces destructans causes WNS. A little brown bat (Myotis lucifugus) with
flagella, and flagella have been identified in members of all flagellum for the bacterial organelle, cilia for the two Read more: Langwig, K.E., et al. 2014. Invasion dynamics of white-nose syndrome fungus,
the white fungal hyphae (arrow) for which WNS is named. midwestern United States, 2012–2014. Emerging Infectious Diseases. 21: 1023–1026.
three domains of life. In fact, the presence of flagella was eukaryotic organelles, and archaellum for the archaeal
long used as a criterion for distinguishing certain protists version of this motility organelle. Will this new name
from others. Recall that protists and other eukaryotic organ- stick? Will the next edition of this text use the term? Will
isms have another motility organelle, the cilium. As the ultra- the discovery that archaeal flagella are evolutionarily re-
especially cellulose and lignin. For example, the common fungus this species are phalloidin and a-amanitin. Phalloidin primarily
structure of eukaryotic flagella and cilia were determined, it lated to bacterial type IV pili lead to a different name? Time
Polyporus squamosus forms large, shelflike structures that attacks liver cells, where it binds to and ruptures plasma mem-
was found that they are the same. Both are very complex and will tell.
project from the lower portion of dead trees, which they help branes. Alpha-amanitin attacks the cells lining the stomach and
make use of microtubules arranged in a characteristic 9 1 2
decompose. Many mushrooms are used as food, and the cultiva- small intestine, causing severe gastrointestinal symptoms asso-
fashion. Furthermore, they move cells in a similar way: by Source: Jarrell, K. F., and Albers, S.-V. 2012. The archaellum: An old motility structure with a
tion of the mushroom Agaricus campestris is a multimillion- ciated with mushroom poisoning. A. muscaria is both poisonous
whipping back and forth. Thus eukaryotic flagella are simply new name. Trends Microbiol. 20(7):307–12.
dollar business. Of course, not all mushrooms are edible. Many and hallucinogenic.
mushrooms produce alkaloids that act as either poisons or hal- Basidiomycetes are named for their characteristic structure
lucinogens. One such example is the “death angel” mushroom, or cell, the basidium, which is involved in sexual reproduction
Amanita phalloides (figure 26.14). Two toxins isolated from (figure 24.15b). A basidium (Greek basidion, small base) is ix
(figure 4.11). The flagellum is not hollow. Hooks have been used to assemble archaeal flagella differs from that used to as-
observed for some archaeal flagella but not for others. These semble pili but that some components may be shared. Bac-
differences have prompted some to suggest a new name for terial flagella (section 3.7)
archaeal flagella—archaella (Microbial Diversity & Ecology 4.1). Despite their similarity to bacterial type IV pili, archaeal
Student-Friendly Organization

3 Micro Focus—Each chapter begins with a real-life story

illustrating the relevance of the content covered in the up-
Bacterial Cell coming text.
Structure
Hooking Up presumed that most other bacteria are like the well-studied model
organisms. However, part of the wonder and fun of science is that nature
is full of surprises. As the biology of more and more bacteria is analyzed,

E ach year over 100 million people around the world become infected
with Neisseria gonorrhoeae, the bacterium that causes gonorrhea.
This troubling statistic is made even more disturbing by the increasing
our understanding of them may change in interesting and exciting ways.

resistance of the bacterium to the antibiotics used to treat the disease.
In males, infection is usually readily detected, but for females, infection
is often asymptomatic and can lead to serious consequences such as
pelvic inflammatory disease (PID) and sterility. These concerns have led
scientists to consider methods for preventing infection. One method is to
block transmission. Unfortunately, relatively little is known about the
transmission process except that it occurs during sexual intercourse and
that numerous hairlike structures (called pili) covering the surface of the
bacterium play a role in establishing infection. The bacterium uses pili
for a type of movement called twitching motility and for adherence to
surfaces such as the sperm and epithelial cells of its human host. It has
long been thought that by attaching to sperm cells the bacterium could
hitch a ride to the female during sexual intercourse. This explained
transmission from male to female. However, it did not clarify how
transmission from female to male occurs.
In 2014 a study reported that exposure of N. gonorrhoeae to seminal
fluid increases its twitching motility and enhances formation of small
aggregates of bacteria. These changes promote infection of host epithelial
cells and, in turn, increase the likelihood that the bacterium will encounter
epithelial tissue of either partner during sexual intercourse. Importantly, this
report helps explain how transmission from female to male might occur. The
study also determined that seminal fluid proteins caused these changes and
suggested that seminal fluid proteins alter the morphology and function of
pili. In particular these proteins cause bundles of pili to separate into single
filaments, enhancing the interaction of bacterial cells with each other and
with host surfaces. Thus, the bacterium sensed the presence of seminal
fluid proteins and responded to them so that it could better effect
transmission and colonization.
Readiness Check:
Readiness Check—The introduction to each chapter in-
Based on what you have learned previously, you should be able to:
✔ Describe the application of small subunit (SSU) rRNA analysis to the
cludes a skills checklist that defines the prior knowledge a
establishment of the three domain classification system proposed by
Carl Woese (section 1.2)
student needs to understand the material that follows.
✔ Identify the following structures or regions of a plant or animal cell and
describe their functions: cell wall, plasma membrane, cytoplasm,
mitochondria, chloroplasts, and ribosomes
✔ Define and give examples of essential nutrients; describe how they
are used by cells
3.1 Use of the Term “Prokaryote” Learning Outcomes—Every section in each chapter begins
Is Controversial
with a list of content-based activities students should be able
After reading this section, you should be able to:
■ List the characteristics originally used to describe prokaryotic cells
■ Form an opinion on the “prokaryote” controversy using current
to perform after reading.
evidence about bacterial cells
Bacteria and archaea have long been lumped together and referred
to as prokaryotes. Although the term was first introduced early in
the twentieth century, the concept of a prokaryote was not fully
outlined until 1962, when R. Stanier and C. B. van Niel described
prokaryotes in terms of what they lacked in comparison to eukary-
otic cells. For instance, Stanier and van Niel pointed out that
prokaryotes lack a membrane-bound nucleus, a cytoskeleton,
membrane-bound organelles, and internal membranous structures
such as the endoplasmic reticulum and Golgi apparatus.
Animation Icon—This
Since the 1960s, biochemical, genetic, and genomic analyses, 6.4 There Are Several Types of Viral Infections 123
6.3 Viral Life Cycles Have Five Steps 121
coupled with improved methods for imaging bacterial and ar-

­symbol indicates that mate-

As this story illustrates, even small, seemingly simple organisms such
chaeal cells, have shown that Bacteria and Archaea are distinct
as bacteria can exhibit complex behaviors. To understand these amazing taxa. Because of this and other discoveries, some microbiologists
reinfected by the wayssameofvirus; thatabout
is, they have immunityFor to Infections of EukaryoticenablingCells
microbes, we must first examine their cell structure and begin to relate it to
rial presented in the text is
question our traditional thinking prokaryotes. plasma membrane, T4 lysozyme to move from the
the functions they carry out. As we consider bacterial cell structure, it is superinfection.
instance, some members Theofsecond is thatphylum
the bacterial as theyPlanctomycetes
reproduce, the pro-
Viruses
cytoplasm cantoharm their eukaryotic host cells in many ways. An
the peptidoglycan.
important to remember that only about 1% of bacterial species have been phagegenetic
have their is replicated
material and inherited
enclosed in by progeny cells.
a membrane; This
other mem-can con-
infection that isresults in cellobserved
death is for a cytocidal infection.
viruses; As
accompanied by an anima-
tinue Budding frequently enveloped in
cultured. Of the cultivated species, only a few have been studied in great bers of thisfor many generations
interesting taxon haveuntil conditions arise organelle
a membrane-bound that cause the
with bacterial formation
fact, envelope and archaeal andviruses, this can
virion release areoccur by concur-
usually lysis of
detail. From this small sample, many generalizations are made, and it is calledprophage to initiate synthesis
the anammoxosome. of phageisproteins
This organelle the site and to assemble
of anoxic the
rent host (figureWhen
processes. Infection
6.17a).virions are does not by
released always resultthe
budding, in lysis
host

42
new virions, a process called induction. Induction is commonly
caused by changes in growth conditions or ultraviolet irradiation
of
cellhost
maycells.
persistent
All envelopes
surviveSome
infections
andviruses
of animal
continue
lasting
(e.g.,
many
viruses
herpesviruses)
releasing
areyears
virions for
(figure
derived from
can
6.17b,c).
establish
some time.
Eukary-
host cell mem-
tion within Instructor Re-
of the host cell. As a result of induction, the lysogenic cycle ends
and the lytic cycle commences; the host cell lyses and progeny
phage particles are released.
otic
branesviruses
changes
by a can
incorporated
cause process.
multistep
or abnormalities
microscopic
into the membrane. in host
First,orvirus-encoded
cells
Then
macroscopic degenerative
theand
proteins are
in tissues isthat
nucleocapsid are
simul- sources in Connect. Create a
distinct from lysis. and
These theare called cytopathic effects (CPEs).
file attachment assignment in
Another important outcome of lysogeny is lysogenic conver- taneously released envelope formed by membrane bud-
Viruses
ding (figureuse 6.15).
a variety of mechanisms
In several virus families, to cause cytopathic
a matrix (M) proteinand
sion. This occurs when a temperate phage changes the phenotype 8/8/15 7:21
wiL81590_ch03_042-079.indd 42 cytocidal
attaches
PM toeffects. Many membrane
the plasma of these areand noted
aidsininchapter
budding. 38.Most
One
of its host. Lysogenic conversion often involves alteration in sur-
face characteristics of the host. For example, when a member of
mechanism
envelopes arise of particular
from thenote is that
plasma some viruses
membrane. Thecause the host
endoplasmic Connect to have your stu-
Micro Inquiry—Selected the genus Salmonella is infected by epsilon phage, the phage
cell to be transformed
reticulum, Golgi apparatus, into a malignant
and other cell (figure
internal 6.17d). This
membranes is
also
changes
Figurethe activities
Releaseofofseveral enzymes
by Lysis involved
of the HostinCell.
construction
discussed
can be used next.
to form envelopes. Mechanism for Releasing
dents view the animation, or
figures in every chapter con-
6.14 T4 Virions The Enveloped Virions
of host
the carbohydrate
cell has been lysed component ofportion
(upper right the bacterium’s lipopolysaccha-
of the cell) and virions have
Viruses and Cancer
post it to your Learning Man-
ride. This eliminates Interestingly, some viruses are not released from their host
been released into the the receptor Progeny
surroundings. for epsilon
virionsphage, sobe
also can theseen
bacte-
cell into the surrounding environment. Rather,problems
their virions move
tain probing questions, add- rium
in thebecomes
cytoplasm.immune
In addition,toempty
infection
capsidsbyof the
another epsilon
infecting virus phage. Cancer is one
from nations,
one hostand
of the most
cellit directly
serious medical
to another host cell.amount
in devel-
Most fungal
Other lysogenic
particles coat theconversions
outside of the give the host pathogenic properties.
cell (336,500). oped is the focus
search. A tumor is a growth phase
viruses lack an extracellular
of an immense
in oftheir replicative
of re-
resultingcycles. agement System for students.
ing another assessment
This is the case when Corynebacterium diphtheriae, the cause of or lump tissue from
MICRO INQUIRY
diphtheria, is infectedWhy do the
with phageemptyb. capsids
The phageremaingenome
attachedencodes
to the Instead they are transmitted
neoplasia—unregulated by cell division,
abnormal new cell spore growth formation,
and repro- or
cell after the
diphtheria viral genome
toxin, which is enters the host cell?
responsible for the disease. Thus only during mating.
duction. TumorVaccinia
cells have viruses elicitshapes
aberrant the formation of long
and altered actin
plasma
opportunity for the student. those strains of C. diphtheriae that are infected by the phage (i.e.,
lysogens) cause disease. Diphtheria (section 39.1)
tails
gens).
that propel nucleocapsids
adjacent
changes cell.from
result
through
membranes that may contain distinctive molecules (tumor anti-
directlyThese
into an In thistheway,
tumor
the plasma
thecells
membrane,
virusbecoming
avoids detec-less
Clearly the infection of a bacterium by a temperate phage tion by the hostTheir
differentiated. immune system. The
unregulated genomes or
proliferation andnucleocapsids
loss of dif-
viruses and some nonenveloped animal viruses. This process of many plant viruses also move directly
has significant impact on the host, but why would viruses ferentiation result in invasive growth thatfrom
forms cell to cell through
unorganized cell
involves the activity of viral proteins. For instance, lysis of small connections called plasmodesmata that link adjacent cells.
evolve this alternate cycle? Two advantages of lysogeny have masses. This reversion to a more primitive or less differentiated
E. coli by T4 requires two specific proteins (figure 6.14). One This spread
been recognized. The first is that lysogeny allows the viral state is calledofanaplasia.
the virus typically involves virus-encoded move-
is lysozyme, an enzyme that attacks peptidoglycan in the host’s ment proteins. The eukaryotic cytoplasm contains a com-
nucleic acid to be maintained within a dormant host. Bacteria Two major types of tumor growth patterns exist. If the tumor
cell wall. The other, called holin, creates holes in E. coli’s plex
often become dormant due to nutrient deprivation, and while in cellscytoskeleton
remain in place and many membranous
to form a compact organelles
mass, the (section
tumor5.3) is
this state, they do not synthesize nucleic acids or proteins. In benign. In contrast, cells from malignant or cancerous tumors
such situations, a prophage would survive but most virulent actively spread throughout the body in a process known as
Viral nucleocapsid
bacteriophages would not be replicated, as they require active metastasis. Some cancers are not solid but cell suspensions. For
cellular biosynthetic machinery. Furthermore, their genome example, leukemias are composed of undifferentiated malignant
Hemagglutinin
would be degraded as the host cell entered dormancy. The sec- white blood cells that circulate throughout the body. Indeed,
ond advantage arises when there are many more phages in an dozens of kinds of cancers arise from a variety of cell types and
environment than there are host cells, a situation virologists afflict all kinds of organisms.
Cross-Referenced Notes— refer to as a high multiplicity of infection (MOI). In these con-
ditions, lysogeny enables the survival of infected host cells
Some viruses have been shown to cause cancer in ani-
mals, including humans; it is estimated that about 10 to 20%
In-text references refer stu- within a population that has few uninfected cells. When MOI is
high, a virulent phage would rapidly destroy the available host
of human cancers have a viral etiology. To understand the role
viruses play in cancer, we must begin by considering carcino-

dents to other parts of the cells in its environment. However, a prophage will be replicated
as the host cell reproduces.
genesis when viruses are not involved. Carcinogenesis is a
complex, multistep process caused by mutations in multiple Retrieve, Infer, Apply—
book to review.
Archaeal viruses can also be virulent or temperate. In addi- genes. Some Budding mutations lead toFree theinfectious
unregulated proliferation
tion, many archaeal viruses establish chronic infections. Unfor-
tunately, little is known about the mechanisms they use to regulate
Viral
that is a major
virion characteristic ofvirion a cancer cell. Other mutations
with envelope
are needed to allow that cell to grow into a cancerous tumor. Questions within the narra-
their replicative cycles. Archaeal viruses (section 27.2)
matrix
protein
For instance, one type of mutation promotes the growth of blood
Neuraminidase
vessels (called angiogenesis) in the developing tumor so that it tive of each chapter help
can obtain needed nutrients Neck and oxygen to support its growth.
students master section con-
Viral envelope proteins Nucleocapsids (only one Plasma membrane of the protruding
Retrieve, Infer,are Apply
inserted into host is shown) are directed Inprotrudes
addition, mutations
outward and that membrane
promote ismetastasis
pinched must occur,
1. Define the terms cell's plasmatemperate
lysogeny, membrane. to the plasma
phage, lysogen, prophage, sonucleocapsids
that the tumor are can invade other
off and tissues.
a mature virlon Mutations
cepts before moving on to
The viral matrix protein lines membrane by host cell's surrounded by matrix- is released.
immunity, and induction.
the cytoplasmic face of
(section 16.1)
microtubules (not lined plasma
2. What advantages might a phage
the plasma gain by being shown).
membrane. capable of lysogeny? Considerable
membrane. research into the causes of cancer has focused
3. Describe lysogenic conversion and its significance. on the mutations that allow cancerous cells to grow uncontrollably.
Figure 6.15 Release of Influenza Virus Virions by Budding. For simplicity, only one of the seven to eight possible nucleocapsids are shown. other topics.

x wiL81590_ch06_109-131.indd 123 21/08/15 10:04 PM

wiL81590_ch06_109-131.indd 121 21/08/15 10:04 PM
 Student-Friendly Organization

52 CHAPTER 3 | Bacterial Cell Structure

Vivid Instructional Art Program—Three-dimensional renditions Bacteria often have more than one transport system Phosphate is then transferred

and bright, attractive colors enhance learning. for a nutrient, as can be seen with E. coli. This bacterium
has at least five transport systems for the sugar galactose,
to incoming sugar via EIIB.
Mannitol-1-P
three systems each for the amino acids glutamate and leu-
cine, and two potassium transport complexes. When sev-
eral transport systems exist for the same substance, the P P
systems differ in such properties as their energy source,

~
~
Mannitol
IIA IIB IIC
their affinity for the solute transported, and the nature of
their regulation. This diversity gives the bacterium an
added competitive advantage in a variable environment.
PEP EI HPr~ P Glucose-6-P
Group Translocation
The distinguishing characteristic of group translocation P P
Pyruvate EI~ P HPr
is that a molecule is chemically modified as it is brought

~
~
IIA Glucose

Annotated Figures—All key metabolic pathways and m ­ olecular

The high-energy phosphate of IIB IIC
into the cell. The best-known group translocation system PEP is transferred via EI to
is the phosphoenolpyruvate: sugar phosphotransfer- HPR and from HPR to EIIA.
ase system (PTS), which is observed in many bacteria.
processes are annotated, so that each step is clearly illustrated The PTS transports a variety of sugars while phosphory-
lating them, using phosphoenolpyruvate (PEP) as the
Cytoplasm Periplasm

and explained. phosphate donor. PEP is an important intermediate of a

biochemical pathway used by many bacteria to extract
Figure 3.14 Group Translocation: Bacterial PTS Transport. Two examples of the
phosphoenolpyruvate: sugar phosphotransferase system (PTS) are illustrated. The
energy from organic energy sources. PEP is a high- following components are involved in the system: phosphoenolpyruvate (PEP), enzyme I
energy molecule that can be used to synthesize ATP, the (EI), the low molecular weight heat-stable protein (HPr), and enzyme II (EII). EIIA is attached
cell’s energy currency. However, when it is used in PTS to EIIB in the mannitol transport system and is separate from EIIB in the glucose system.
reactions, the energy present in PEP is used to energize
NK cell
sugar uptake rather than ATP synthesis. ATP (sec-
tion 10.2); Embden-Meyerhof pathway (section 11.4) Green - Fe31
The transfer of phosphate from PEP to the incoming molecule Red - O
nanotubes involves several proteins and is an example of a phosphorelay Gray - C
system. In E. coli and Salmonella, the PTS consists of two en- Blue - N
zymes and a low molecular weight heat-stable protein (HPr). A White - H
phosphate is transferred from PEP to enzyme II with the aid of
MHC and Adhesion
enzyme I and HPr (figure 3.14). Enzyme II then phosphorylates
Receptor Binding the sugar molecule as it is carried
cytoskeleton NK cellacross
abuts target
the membrane. Many
re-arrangement forming a lytic cleft
(a) Target cell (b) different PTSs exist, and (c) they vary in terms of the sugars they
results in firm
transport.ofThe
attachment NK specificity lies with the type of Enzyme II used in
theand
cell PTS. Enzyme I and HPr are the same in all PTSs used by a
granule
relocation
bacterium. Enzymes and ribozymes speed up cellular
chemical reactions (section 10.6) Figure 3.15 Enterobactin: A Siderophore Produced by E. coli. Ball-
PTSs are widely distributed in bacteria, being found primar- and-stick model of enterobactin complexed with Fe31.
ily among facultatively anaerobic bacteria (bacteria that grow in
either the presence or absence of O2); some obligately anaerobic
bacteria (e.g., Clostridium spp.) also have PTSs. However, most Iron Uptake
aerobic bacteria lack PTSs. Many carbohydrates are transported Almost all microorganisms require iron for building molecules im-
by PTSs. E. coli takes up glucose, fructose, mannitol, sucrose, N- portant in energy-conserving processes (e.g., cytochromes), as well
acetylglucosamine, cellobiose, and other carbohydrates by group as for the function of many enzymes. Iron uptake is made difficult
translocation. Besides their role in transport, PTSs function in by the extreme insolubility of ferric iron (Fe31) and its derivatives,
numerous regulatory processes, including Dead the regulation of car- which leaves little free iron available for transport. Many bacteria
NK lytic granules are perforins granzymes One example istarget cell
released into cleft bonandmetabolism. the role of PTSs in catabolite have overcome this difficulty by secreting siderophores (Greek for
(d) (e) lyse target cell (f)
Key Concepts 417 repression, a phenomenon in which the cell inhibits synthesis of iron bearers). Siderophores are low molecular weight organic mol-
Figure 33.12 The System Used by Natural Killer (NK) Cells to Recognize degradative
and Destroyenzymes
Abnormalfor some(a)sugars
Cells. NK cell so that ittarget
evaluates can cell
catabolize a
using membrane ecules that bind ferric iron and supply it to the cell (figure 3.15).
nanotubes. (b) Microtubules organize lytic granules toward the target cell. (c)preferred sugar.
A lytic cleft formsWe
and describe
(d) granulesthis
exitinthe
more detail
NK cell into in
thechapter
cleft. (e) 14.
LyticPTS
perforins and Electron transport chains (section 10.4); Enzymes and ribo-
granzymes lyse the target cell. (f) The NK cell releases the dead target cell andproteins also
migrates can bind
toward chemical
another cell. attractants, toward which bacteria zymes speed up cellular chemical reactions (section 10.6)
move by the process of chemotaxis (p. 74). Oxygen concen- Microorganisms secrete siderophores when iron is scarce in
Key Concepts Cytotoxic (killer) ILCs are represented by natural killer tration (section 7.4) Active Transport by Group Translocation the medium. Once the iron-siderophore complex has reached the
■ Once the recombinant plasmid has Natural
cells. been introduced
killer (NK) cells are a small population of large, Antibodies Target cell infected
17.1 Key Discoveries Led to the Development of
Recombinant DNA Technology into host cells, cells carrying nonphagocytic
vector must be selected.
granular lymphocytes. The major NK cell func- with virus
This is often accomplished bytion allowing the growth
is to detect of
and destroy stressed, malignant, or virally in- Virus antigen
■ Genetic engineering became possible after the discovery only antibiotic-resistant cells fected
becausecellsthe vector
(figurebears an Although the exact mechanism by
33.12).
of restriction enzymes and reverse transcriptase, and the antibiotic-resistance gene. Cells thatNK tookcells
up vector with target cells is not known, it is clear 1
which recognize
development of essential methods in nucleic acid chemistry inserted DNA must then be distinguished fromadjacent
those that
that they survey cells by forming membrane nanotube
such as the Southern blotting technique. contain only vector. Often a blue-versus-white colony
connections, and by “kissing” targets via several surface receptors
wiL81590_ch03_042-079.indd 52
(a) 8/8/15 7:21 PM
Restriction enzymes are important because they cut DNA
Key Concepts—At the end of each chapter and organized
■
phenotype is used; this is based on the33.12a).
(figure presence or absence,
These interactions provide both kill and don’t
at specific sequences, thereby releasing fragments of DNA respectively, of a functional lacZ
kill gene
signals(figure
to the17.11).
NK cell. It is the balance of these signals that Antibody receptor
that can be cloned or otherwise manipulated (figure 17.3

■
and table 17.1).
Gel electrophoresis is used to separate molecules according
17.4 Introducing RecombinantbeDNA
determines the fate of the target cell. If the target cell is found to
into or
defective Host Cells the NK cell kiss becomes deadly.
infected, by numbered headings, this feature distills the content to
Target cell infected
with virus now coated
with antibody
■ The bacterium E. coli and the yeast are the
Once activated to kill the target cell, the NK cell mobilizes
S. cerevisiae
■
to charge and size.
DNA fragments are separated on agarose and acrylamide
most common host species. its cytoskeletal proteins to form an “immunological synapse,”
■ DNA can be introduced into microbes
similar tobythe transformation
synapses cytotoxic lymphocytes form with their
its essential components with cross-references to ­figures
gels. Because DNA is acidic, it migrates from the negative
to the positive end of a gel (figure 17.6).
or electroporation. targets. When kill signals are activated, the NK cell closely ad-
heres to the target cell and releases its cargo of deadly molecules
and tables.
NK cell
17.2 Polymerase Chain Reaction Amplifies 17.5 Genomic Libraries: Cloning Genomes
(figure in Pieces
33.12). These include the pore-forming protein perforin
(b)
Targeted DNA ■ It is sometimes necessary to findand aenzymes calledthe
gene without granzymes. Together, these proteins trigger
■ The polymerase chain reaction (PCR) allows small knowledge of the gene’s DNAthe target cell
sequence. to commit
A genomic suicide (apoposis).
library
NK cells
is constructed by cleaving an organism’s also have
genome intoanother
many killing mechanism. NK cells have Target cell lysis
amounts of specific DNA sequences to be amplified, or
receptors
fragments, each of which is cloned intofor antibodies,
a vector and atherefore can attack cells that are op-
to make
increased in concentration thousands of times (figure 17.8).
■ PCR consists of multiple cycles of 3 steps each: DNA unique recombinant plasmid. sonized by antibodies. This process is called antibody-dependent
cell-mediated
■ Genomic libraries are often screened for the cytotoxicity
gene (ADCC) (figure 33.13), and the
denaturation, primer annealing, and DNA synthesis. Granzymes
■ PCR has numerous applications. It often is used to of interest by either phenotypic rescue (genetic and perforins
obtain genes for cloning and in diagnostic and forensic complementation) or DNA hybridization
Figure 33.13with an
Antibody-Dependent Cell-Mediated Cytotoxicity. (a) In this
science. oligonucleotide probe (figuremechanism,
17.13). antibodies bind to a target cell infected with a virus. (b) NK cells have NK cell
specific antibody receptors on their surface. (c) The antibody bridges the infected
17.3 Cloning Vectors Are Needed to Create 17.6 Expressing Foreign Genes
cellin
withHost
the NKCells
cell so that the target is close enough for enzymatic attack. (c)
Recombinant DNA ■ An expression vector has the necessary features to express
■ There are four types of cloning vectors: plasmids, viruses, in high levels any recombinant gene it carries. 723
cosmids, and artificial chromosomes. Cloning vectors ■ If a eukaryotic gene is to be expressed in a bacterium,
generally have at least three components: an origin of cDNA is used because it lacks introns; a bacterial leader
replication, a selectable marker, and a multicloning site must also be added to the 59 end of the gene.
or polylinker (table 17.2; figures 17.10 and 17.12). ■ Purification of recombinant proteins is often accomplished
■ The most common approach to cloning is to digest both by fusing the coding sequence of a 723
wiL81590_ch33_707-735.indd protein to six histidine 9/3/15 2:34 PM

vector and DNA to be inserted with the same restriction
enzyme or enzymes so that compatible sticky ends are
generated. The vector and DNA to be cloned are then
incubated in the presence of DNA ligase, which catalyzes
the formation of phosphodiester bonds once the DNA
fragment inserts into the vector.
residue codons found on some expression vectors. When
introduced and expressed in bacteria, the His-tagged protein
can be selectively purified (figure 17.14).
■ Green fluorescent protein can be used to study the regulation
of gene expression (transcriptional fusions) and protein
localization (translational fusions) (figure 17.15).

Compare, Hypothesize, Invent—Includes questions taken

Compare, Hypothesize, Invent from current literature; designed to stimulate analytical
1. You are performing a PCR to amplify a gene encoding a
tRNA from a bacterium that has only recently been grown
2. You have cloned a structural gene required for riboflavin
synthesis in E. coli. You find that an E. coli riboflavin problem-solving skills.
in pure culture. You are expecting a product of 954 bp. auxotroph carrying the cloned gene on a vector makes
However, you generate three different products; only one less riboflavin than does the wild-type strain. Why might
is the expected size. List at least two possible explanations this be the case?
(excluding experimental error).

wiL81590_ch17_400-418.indd 417 8/18/15 4:58 AM

xi
List of Content Changes
Each chapter has been thoroughly reviewed.
Part One
Chapter 1—Evolution is the driving force of all biological sys-
tems; this is made clear by introducing essential concepts of mi-
crobial evolution first. Advances in the discipline of microbiology
and the increasing contributions of genomics and metagenomics
are discussed.
Chapter 2—Microscopy was and is critical to the study of
­micro­organisms and this chapter considers the most commonly
used methods, including expanded coverage of phase-contrast
microscopy.
Chapter 3—Coverage of bacterial cellular structure and func-
tion. A new chapter-opening story clearly establishes the impor-
tance of the material covered in this chapter.
Chapter 4—Growing understanding of the distinctive charac-
teristics of archaea has warranted the creation of a new Micro-
bial Diversity & Ecology box on the nature of motility
organelles in the three domains of life. Comparisons to bacte-
ria are made throughout the chapter.
Chapter 5—An introduction to eukaryotic cell structure and
function, with emphasis on eukaryotic microbes. More detailed
information on protist and fungal cells is presented in chapters 25
(Protists) and 26 (Fungi), which also focus on the diversity of
these microbes. The current thought on the evolution of mito-
chondria and mitochondria-like organelles is considered. Com-
parisons between bacteria, archaea, and eukaryotes are included
throughout the chapter.
Chapter 6—This chapter surveys the essential morphological,
physiological, and genetic elements of viruses as well as vi-
roids, satellites, and prions. Updated discussion of the role of
viruses in causing cancer. This chapter completes our four-
chapter introduction to microbial life.
Part Two
Chapter 7—Discussion of the growth of microbes outside the
laboratory, including expanded and updated coverage of the “per-
sister cell” phenomenon, is followed by topics related to labora-
tory culture of microbes.
Chapter 8—Updated to reflect emphasis on interruption of nor-
mal growth and reproduction functions to control microorganisms.
Chapter 9—Content focuses on the mechanism of action of each
antimicrobial agent and stresses usage to limit drug resistance.
xii
Part Three
Chapter 10—This introduction to metabolism includes a section
outlining the nature of biochemical pathways. The concept of
metabolic flux is presented by discussing the interconnected bio-
chemical pathways used by cells.
Chapter 11—An introduction to metabolic diversity and nutri-
tional types is followed by an exploration of the energy-conserving
process of each nutritional type. The coverage of oxygenic pho-
tosynthesis is expanded and updated.
Chapter 12—New coverage of pathways used to synthesize por-
phyrins, lipopolysaccharides, sterols, and isoprenoid lipids.
Part Four
Chapter 13—Updated coverage of protein splicing, folding, and
secretion.
Chapter 14—The regulation of bacterial cellular processes, with
updated coverage of regulation by small RNAs.
Chapter 15—Eukaryal and archaeal genome replication and ex-
pression are considered together. In both cases, the discussion
has been updated and expanded, and reflects the similarity of
information flow as carried out by members of Archaea and
­Eukarya.
Chapter 16—Covers mutation, repair, and recombination in the
context of processes that introduce genetic variation into popula-
tions. A new chapter-opening story introduces the complexity of
understanding the growing problem of antibiotic resistance.
Chapter 17—Students are guided through the steps of cloning
a microbial gene—from DNA purification through protein
­purification.
Chapter 18—Next-generation nucleotide sequencing and single-
cell genome sequencing are covered in the context of meta­
genomics as it relates to the microbial ecology of natural systems,
including the human microbiome.
Part Five
Chapter 19—This overview of microbial evolution includes
­discussion of the concepts of ecotype, microbial species, and
superphylum.
Chapter 20—Expanded coverage of archaeal physiology in-
cludes archaeal-specific catabolic and anabolic pathways with
particular attention CO2 fixation. The evolutionary advantage of
each pathway is discussed in the context of archaeal ecology.
 List of Content Changes
Chapter 21—In addition to the ecology and physiology of
photo­synthetic bacteria, the recently described Planctomycetes,
Verrucomicrobia, Chlamydia (PVC) superphylum is introduced
with an updated review of each of these genera.
Chapter 22—This chapter’s coverage includes newly recognized
genera, an expanded discussion of sulfur metabolism, and an up-
dated discussion of gliding motility that reflects recent advances.
Chapter 24—This overview of actinobacteria incorporates
new figures illustrating the mycobacterial cell wall and a new
photo program.
Chapter 25—This chapter introduces protist morphology and
diversity, with an emphasis on physiological adaptation and
ecology.
Chapter 26—Fungal diversity is presented within a phylogenetic
framework. Morphology, ecology, and reproductive strategies
are stressed.
Chapter 27—Updated discussion of virus taxonomy and phylogeny.
Part Six
Chapter 28—The description of each nutrient cycle is accompa-
nied by a “student-friendly” figure that distinguishes between
reductive and oxidative reactions. Updated coverage of the role
of biogeochemical cycling in global climate change.
Chapter 29—This chapter continues to emphasize culture-based
techniques as the “gold standard” and reviews some new, innova-
tive approaches such as mass spectrometry in the identification
of microbial taxa as well as metatranscriptomics and meta­
proteomics in the study of community activity.
Chapter 30—Updated and expanded discussion of the role of
marine microbes in the global carbon budget as well as an update
on subsurface microbes.
Chapter 31—New and updated coverage of the microbial ecol-
ogy of the phyllosphere, rhizoplane, and rhizosphere. Expanded
discussion of fungal plant pathogens.
Chapter 32—Important model systems for the exploration of
microbial symbiosis are presented, along with increased cover-
age of the human microbiome.
Part Seven
Chapter 33—Updated to reflect the increasing overlap with the
acquired immune functions, this chapter on innate host resistance
provides in-depth coverage of physical and chemical components
of the nonspecific host response, followed by an overview of
cells, tissues, and organs of the immune system. Uniting these
components are the ever-expanding methods for recognition of
microorganisms by immune cells. Barriers, chemical mediators,
and immune cells define the molecular mechanisms that drive
phagocytosis and inflammation.
Chapter 34—Updated to enhance linkages between innate and
adaptive immune activities. Discussions integrate concepts of
cell biology, physiology, and genetics to present the immune sys-
tem as a unified response having various components. Implica-
tions of dysfunctional immune actions are also discussed.
Chapter 35—This chapter has been reorganized to reflect the
host-microorganism interaction that can lead to human disease.
The essential elements required for a pathogen to establish infec-
tion are introduced, and virulence mechanisms are highlighted.
This chapter is placed after the immunology chapters to stress
that the host-parasite relationship is dynamic, with adaptations
and responses offered by both host and parasite.
Part Eight
Chapter 36—This chapter has been updated to reflect the tech-
nological advances of a modern clinical laboratory. Emphasis is
on modern diagnostic testing to identify infectious disease.
Chapter 37—Expanded focus on the important role of labora-
tory safety, especially in the teaching laboratory. Discussion em-
phasizes modern epidemiology as an investigative science and its
role in preventative medicine. Disease prevention strategies are
highlighted.
Chapter 38—Updated and expanded coverage includes viral patho-
genesis, common viral infections, and prion-mediated diseases.
Chapter 39—Updated coverage of bacterial organisms and the
ways in which they commonly lead to human disease.
Chapter 40—Updated and expanded coverage of fungal and pro-
tozoal diseases.
Part Nine
Chapter 41—Discussion of milk fermentation processes, includ-
ing an updated description of cheese making.
Chapter 42—Includes updated coverage of biofuel production
(first introduced in chapter 21) and an introduction to synthetic
biology.
Chapter 43—This chapter complements our 21st-century ap-
proach to microbiology by emphasizing the importance of clean
water and the power of microbial environmental remediation.
xiii
Lab Tools for Your Success

LearnSmart Labs® is an adaptive simulated lab experience that brings

meaningful scientific exploration to students. Through a series of adaptive
questions, LearnSmart Labs identifies a student’s knowledge gaps and provides
resources to quickly and efficiently close those gaps. Once students have
mastered the necessary basic skills and concepts, they engage in a highly
realistic simulated lab experience that allows for mistakes and the execution
of the scientific method.

LearnSmart® Prep is an adaptive learning tool that prepares students for

college-level work in Microbiology. LearnSmart Prep individually identifies
concepts the student does not fully understand and provides learning resources
to teach essential concepts so he or she enters the classroom prepared. Data-
driven reports highlight areas where students are struggling, helping to
accurately identify weak areas.

Laboratory Exercises in Microbiology, Tenth Edition

John P. Harley has revised this laboratory manual to accompany the tenth edition of Prescott’s
Microbiology. The class-tested exercises are modular which allows instructors to easily incorporate them
into their course. This balanced introduction to each area of microbiology also has accompanying Connect
content for additional homework and assessment opportunities. In addition, all artwork from the lab
manual is available through the Instructor Resources in Connect for incorporation into lectures.

Acknowledgments

In the preparation of each edition, we have been guided
by the collective wisdom of reviewers who are expert
microbiologists and excellent teachers. They represent
experience in community colleges, liberal arts colleges,
comprehensive institutions, and research universities. We
have followed their recommendations, while remaining
true to our overriding goal of writing readable, student-
centered content. Each feature incorporated into this edition
has been carefully considered in terms of how it may be used
to support student learning in both the traditional and the
flipped learning environment.
Also in this edition, we are very excited to incorporate
real student data points and input, derived from thousands of
our LearnSmart users, to help guide our revision. With this
information, we were able to hone both book and digital content.
The authors wish to extend their gratitude to our team at
McGraw-Hill, including Marija Magner, Darlene Schueller,
Kristine Rellihan, Jayne Klein, Tara McDermott, Christina
Nelson, Lorraine Buczek, Carrie Burger, and David Tietz.
Finally, we thank our spouses and children, who provided
support and tolerated our absences (mental, if not physical)
while we completed this demanding project.

xiv
 Contents

3.7 Many Bacteria Have External Structures

Part One Introduction to Microbiology Used for Attachment and Motility 68
3.8 Bacteria Move in Response to
1 The Evolution of Microorganisms and
Environmental Conditions 71
Microbiology 1
3.9 Bacterial Endospores Are a Survival
Micro Focus: Strategy 75
Over 4,000 Potential Planets Discovered 1
1.1 Members of the Microbial World 1 4 Archaeal Cell Structure 80
1.2 Microbes Have Evolved and Diversified for Micro Focus:
Billions of Years 4 Cows and Buffaloes and Sheep,
1.3 Microbiology Advanced as New Tools for Oh My! 80
Studying Microbes Were Developed 11
4.1 Archaea Are Diverse but Share Some
1.4 Microbiology Encompasses Many
Common Features 80
Subdisciplines 17
4.2 Six Major Types of Archaeal Cell
Envelopes Have Been Identified 82
2 Microscopy 22
4.3 Archaeal Cytoplasm Is Similar to
Micro Focus: Bacterial Cytoplasm 85
Anthrax Bioterrorism Attack 2001 22 4.4 Many Archaea Have External Structures
2.1 Lenses Create Images by Bending Light 22 Used for Attachment and Motility 86
2.2 There Are Several Types of Light Microbial Diversity & Ecology 4.1
Microscopes 23 What’s in a Name? 87
2.3 Staining Specimens Helps to Visualize and 4.5 Comparison of Bacteria and Archaea 88
Identify Microbes 32
2.4 Electron Microscopes Use Beams of 5 Eukaryotic Cell Structure 90
Electrons to Create Highly Magnified
Micro Focus: Red Means Dead 90
Images 34
2.5 Scanning Probe Microscopy Can Visualize 5.1 Eukaryotic Cells Are Diverse but
Molecules and Atoms 39 Share Some Common Features 90
5.2 Eukaryotic Cell Envelopes 92
3 Bacterial Cell Structure 42 5.3 The Eukaryotic Cytoplasm Contains
a Complex Cytoskeleton and Many
Micro Focus: Hooking Up 42
Membranous Organelles 93
3.1 Use of the Term “Prokaryote” Is
5.4 Several Cytoplasmic Membranous
Controversial 42
Organelles Function in the Secretory
3.2 Bacteria Are Diverse but Share Some
and Endocytic Pathways 95
Common Features 43
5.5 The Nucleus and Ribosomes Are
3.3 Bacterial Plasma Membranes Control
Involved in Genetic Control of the Cell 98
What Enters and Leaves the Cell 47
5.6 Mitochondria, Related Organelles, and
3.4 There Are Two Main Types of
Chloroplasts Are Involved in Energy
Bacterial Cell Walls 53
Conservation 100
Microbial Diversity & Ecology 3.1
Microbial Diversity & Ecology 5.1
Gram Positive and Gram Negative or
Monoderms and Diderms? 54 There Was an Old Woman Who
Swallowed a Fly 103
3.5 The Cell Envelope Often Includes Layers
5.7 Many Eukaryotic Microbes Have
Outside the Cell Wall 61
External Structures Used for Motility 104
3.6 The Bacterial Cytoplasm Is More
5.8 Comparison of Bacterial, Archaeal,
Complex than Once Thought 62
and Eukaryotic Cells 105

xv
Contents

6 Viruses and Other Acellular Infectious Agents 109 8.2 The Pattern of Microbial Death Mirrors
Micro Focus: the Pattern of Microbial Growth 174
Mustard, Catsup, and Viruses? 109 8.3 Mechanical Removal Methods Rely
on Barriers 175
6.1 Viruses Are Acellular 109
8.4 Physical Control Methods Alter
Microbial Diversity & Ecology 6.1
Microorganisms to Make Them
Host-Independent Growth of an Archaeal Virus 110
Nonviable 177
6.2 Virion Structure Is Defined by Capsid 8.5 Microorganisms Are Controlled with
Symmetry and Presence or Absence of Chemical Agents 180
an Envelope 111 8.6 Antimicrobial Agents Must Be Evaluated
6.3 Viral Life Cycles Have Five Steps 116 for Effectiveness 184
6.4 There Are Several Types of Viral Infections 122 8.7 Microorganisms Can Be Controlled by
6.5 Cultivation and Enumeration of Viruses 125 Biological Methods 185
6.6 Viroids and Satellites: Nucleic
Acid-Based Subviral Agents 127 9 Antimicrobial Chemotherapy 188
6.7 Prions Are Composed Only of Protein 129 Micro Focus:
A Teaspoon of Sugar Helps the Bacteria
Go Down 188
Part Two M
 icrobial Nutrition, Growth,
9.1 Antimicrobial Chemotherapy Evolved
and Control
from Antisepsis Efforts 188
7 Microbial Growth 132 9.2 Antimicrobial Drugs Need to Be Selectively
Toxic over a Range of Effectiveness 189
Micro Focus: Metal or Plastic? 132
9.3 Antimicrobial Activity Can Be Measured
7.1 Most Bacteria and Archaea Reproduce
by Specific Tests 192
by Binary Fission 132
9.4 Antibacterial Drugs 194
7.2 Bacterial Cell Cycles Can Be Divided
9.5 Antifungal Drugs 200
into Three Phases 133
9.6 Antiviral Drugs 200
7.3 Some Archaeal Cell Cycles Resemble
9.7 Antiprotozoan Drugs 204
the Eukaryotic Cell Cycle 140
9.8 Several Factors Influence Antimicrobial
7.4 Environmental Factors Affect Microbial
Drug Effectiveness 205
Growth 141
7.5 Microbial Growth in Natural Environments 150
7.6 Laboratory Culture of Cellular Microbes
Requires Media and Conditions That
Mimic the Normal Habitat of a Microbe 154
Part Three Microbial Metabolism
7.7 Growth Curves Consist of Five Phases 161 10 Introduction to Metabolism 208
7.8 Microbial Population Size Can Be
Micro Focus: Flushed Away 208
Measured Directly or Indirectly 164
10.1 Metabolism: Important Principles
7.9 Chemostats and Turbidostats Are Used
and Concepts 209
for Continuous Culture of Microorganisms 168
10.2 ATP: The Major Energy Currency
8 Control of Microorganisms in the of Cells 211
Environment 172 10.3 Redox Reactions: Reactions of Central
Importance in Metabolism 213
Micro Focus:
10.4 Electron Transport Chains: Sets of
Bacterial Kamikazes Seek Out and
Sequential Redox Reactions 214
Destroy Pathogens 172
10.5 Biochemical Pathways: Sets of Linked
8.1 Microbial Growth and Replication Chemical Reactions 217
Pathways: Targets for Control 172

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10.6 Enzymes and Ribozymes Speed Up

Cellular Chemical Reactions 217 Part Four M
 icrobial Molecular Biology and
10.7 Metabolism Must Be Regulated Genetics
to Maintain Homeostasis and
Prevent Waste 222 13 Bacterial Genome Replication and Expression 284
Micro Focus: Making Code 284
11 Catabolism: Energy Release and 13.1 Experiments Using Bacteria and Viruses
Conservation 227 Demonstrated that DNA Is the Genetic
Micro Focus: The Richest Hill On Earth 227 Material 285
11.1 Metabolic Diversity and Nutritional 13.2 Nucleic Acid and Protein Structure 286
Types 227 13.3 DNA Replication in Bacteria 291
11.2 There Are Three Chemoorganotrophic 13.4 Bacterial Genes Consist of Coding
Fueling Processes 229 Regions and Other Sequences Important
11.3 Aerobic Respiration Can Be Divided for Gene Function 298
into Three Steps 232 13.5 Transcription in Bacteria 301
11.4 Glucose to Pyruvate: The First Step 232 13.6 The Genetic Code Consists of
11.5 Pyruvate to Carbon Dioxide (Step 2) Is Three-Letter “Words” 305
Accomplished by the Tricarboxylic 13.7 Translation in Bacteria 308
Acid Cycle 236 13.8 Protein Maturation and Secretion 315
11.6 Electron Transport and Oxidative
Phosphorylation (Step 3) Generate 14 Regulation of Bacterial Cellular Processes 321
the Most ATP 236 Micro Focus: Letting Go 321
11.7 Anaerobic Respiration Uses the Same 14.1 Bacteria Use Many Regulatory Options 322
Three Steps as Aerobic Respiration 244 14.2 Regulation of Transcription Initiation
11.8 Fermentation Does Not Involve an Saves Considerable Energy and Materials 322
Electron Transport Chain 245 14.3 Attenuation and Riboswitches Can
11.9 Catabolism of Organic Molecules Stop Transcription Prematurely 329
Other Than Glucose 248 14.4 Riboswitches and Small RNAs Can
11.10 Chemolithotrophy: “Eating Rocks” 250 Control Translation 332
11.11 Phototrophy 253 14.5 Bacteria Combine Several Regulatory
Mechanisms to Control Complex
12 Anabolism: The Use of Energy in Cellular Processes 334
Biosynthesis 262
Micro Focus: An Author’s Life Saved 262 15 Eukaryotic and Archaeal Genome
12.1 Principles Governing Biosynthesis 262 Replication and Expression 349
12.2 Precursor Metabolites: Starting Micro Focus:
Molecules for Biosynthesis 264 Plastics: Brought to You by Microbes 349
12.3 CO2 Fixation: Reduction and Assimilation 15.1 Why Consider Eukaryotic and Archaeal
of CO2 Carbon 264 Genetics Together? 350
12.4 Synthesis of Carbohydrates 267 15.2 DNA Replication: Similar Overall, but
12.5 Synthesis of Amino Acids Consumes with Different Replisome Proteins 350
Many Precursor Metabolites 270 15.3 Transcription 354
12.6 Synthesis of Purines, Pyrimidines, and 15.4 Translation and Protein Maturation and
Nucleotides 276 Localization 358
12.7 Lipid Synthesis 278 15.5 Regulation of Cellular Processes 364

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16 Mechanisms of Genetic Variation 369 18.4 Bioinformatics: What Does the

Micro Focus: Manure Happens 369 Sequence Mean? 428
16.1 Mutations: Heritable Changes in 18.5 Functional Genomics Links Genes to
a Genome 370 Phenotype 431
16.2 Detection and Isolation of Mutants 375 18.6 Systems Biology: Making and Testing
16.3 DNA Repair Maintains Genome Stability 377 Complex Predictions 437
16.4 Microbes Use Mechanisms Other than 18.7 Comparative Genomics 438
Mutation to Create Genetic Variability 380
16.5 Transposable Elements Move Genes
Within and Between DNA Molecules 382 Part Five The Diversity of the Microbial World
16.6 Bacterial Conjugation Requires 19 Microbial Taxonomy and the Evolution
Cell-Cell Contact 384 of Diversity 443
16.7 Bacterial Transformation Is the Uptake
of Free DNA from the Environment 389 Micro Focus:
16.8 Transduction Is Virus-Mediated Scientists Query: “Is the Microbial
DNA Transfer 391 Universe Expanding?” 443
16.9 Evolution in Action: The Development 19.1 Microbial Taxonomy Is Based on the
of Antibiotic Resistance in Bacteria 394 Evolution of Multiple Traits 444
19.2 Taxonomic Ranks Provide an
17 Recombinant DNA Technology 400 Organizational Framework 445
Micro Focus: 19.3 Microbial Taxonomy and Phylogeny
Archeological Digs Reveal Source Are Largely Based on Molecular
of Ancient Pathogen 400 Characterization 446
17.1 Key Discoveries Led to the Development 19.4 Phylogenetic Trees Illustrate
of Recombinant DNA Technology 401 Evolutionary Relationships 452
19.5 Evolutionary Processes and the Concept
Techniques & Applications 17.1
Streptavidin-Biotin Binding and Biotechnology 405 of a Microbial Species Inspire Debate 455
19.6 Bergey’s Manual of Systematic Bacteriology 460
17.2 Polymerase Chain Reaction Amplifies
Targeted DNA 406 20 Archaea 464
17.3 Cloning Vectors Are Needed to Create Micro Focus:
Recombinant DNA 408 Methanogenic Archaea Fuel Domestic
17.4 Introducing Recombinant DNA into Energy Debate 464
Host Cells 411 20.1 Overview of Archaea 465
Techniques & Applications 17.2 20.2 Phylum Crenarchaeota: Metabolically
How to Build a Microorganism 412 Diverse Thermophiles 471
17.5 Genomic Libraries: Cloning Genomes 20.3 Phylum Thaumarchaeota: Mesophilic
in Pieces 413 Ammonia Oxidizers 474
17.6 Expressing Foreign Genes in Host Cells 414 20.4 Phylum Euryarchaeota: Methanogens,
Haloarchaea, and Others 474
18 Microbial Genomics 419
Micro Focus: 21 Deinococci, Mollicutes, and
“Synthetic Life”: Oxymoron or the Nonproteobacterial Gram-Negative Bacteria 483
Future? 419 Micro Focus:
18.1 DNA Sequencing Methods 419 Cyanobacteria Stimulate Broad Appeal
18.2 Genome Sequencing 424 for Biofuel Production 483
18.3 Metagenomics Provides Access to 21.1 Aquificae and Thermotogae Are Ancient
Uncultured Microbes 427 Bacterial Lineages 484

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21.2 Deinococcus-Thermus Includes 24 Actinobacteria: The High G 1 C Gram-Positive

Radiation-Resistant Bacteria 484 Bacteria 552
21.3 Class Mollicutes, Phylum Tenericutes: Micro Focus:
Bacteria That Lack Cell Walls 485 Antibiotic Production: Is it Actually
21.4 Photosynthetic Bacteria Are Diverse 488 Bacterial Chit-Chat? 552
21.5 Phylum Planctomycetes: Bacteria with 24.1 Class Actinobacteria 554
Intracellular Compartments 495
21.6 Phylum Chlamydiae: Obligate 25 Protists 563
Intracellular Parasites 497 Micro Focus:
21.7 Phylum Verrucomicrobia Includes Sustainable Farming Practiced
Human Symbionts and Methylotrophs 497 by Amoebae 563
21.8 Phylum Spirochaetes: Bacteria with
25.1 Protist Diversity Reflects Broad Phylogeny 564
a Corkscrew Morphology 499
25.2 Supergroup Excavata: Primitive Eukaryotes 566
21.9 Phylum Bacteroidetes Includes
25.3 Supergroup Amoebozoa Includes
Important Gut Microbiota 501
Protists with Pseudopodia 568
25.4 Supergroup SAR: Protists of Great
22 Proteobacteria 504
Importance 570
Micro Focus: 25.5 Supergroup Archaeplastida Includes
Bison and Brucellosis Spark Controversy 504 “Green Algae” 579
22.1 Class Alphaproteobacteria Includes
Many Oligotrophs 505 26 Fungi (Eumycota) 583
22.2 Class Betaproteobacteria Includes Micro Focus:
Chemoheterotrophs and Fungi May Be Key to Quelling Malaria 583
Chemolithotrophs 515 26.1 Fungal Biology Reflects Vast Diversity 585
Microbial Diversity & Ecology 22.1 26.2 Chytridiomycota Produce Motile Spores 588
Acid Mine Drainage 519 26.3 Zygomycota: Fungi with Coenocytic
22.3 Class Gammaproteobacteria Is the Hyphae 588
Largest Bacterial Class 519 26.4 Glomeromycota Are Mycorrhizal Symbionts 589
Microbial Diversity & Ecology 22.2 26.5 Ascomycota Includes Yeasts and Molds 590
Bacterial Bioluminescence 527 26.6 Basidiomycota Includes Mushrooms
and Plant Pathogens 592
22.4 Class Deltaproteobacteria Includes
Disease 26.1
Chemoheterotrophic Anaerobes White-Nose Syndrome Is Decimating
and Predators 529 North American Bat Populations 593
22.5 Class Epsilonproteobacteria Ranges
26.7 Microsporidia Are Intracellular Parasites 595
from Pathogens to Deep-Sea Bacteria 535
27 Viruses 597
23 Firmicutes: The Low G 1 C Gram-Positive
Micro Focus:
Bacteria 539
Deadly New Virus Strikes European
Micro Focus: Farm Animals 597
Invasive Strep Strikes Young, Old, 27.1 Virus Phylogeny Is Difficult to Establish 597
and Famous 539 27.2 Double-Stranded DNA Viruses Infect
23.1 Class Clostridia: Anaerobic All Cell Types 599
Endospore-Forming Bacteria 540 Microbial Diversity & Ecology 27.1
23.2 Class Negativicutes: Gram-Positive What Is a Virus? 609
Bacteria with Outer Membranes 544 27.3 Single-Stranded DNA Viruses Use
23.3 Class Bacilli: Aerobic Endospore- a Double-Stranded Intermediate in
Forming Bacteria 544 Their Life Cycles 610
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Contents

27.4 Double-Stranded RNA Viruses: RNA- 31.2 Diverse Microorganisms Inhabit Soil 669
Dependent RNA Polymerase Replicates 31.3 Microbe-Plant Interactions Can Be
the Genome and Synthesizes mRNA 611 Positive, Negative, or Neutral 671
27.5 Plus-Strand RNA Viruses: Genomes 31.4 The Subsurface Biosphere Is Vast 683
That Can Be Translated upon Entry 613
27.6 Minus-Strand RNA Viruses: RNA-Dependent 32 Microbial Interactions 685
RNA Polymerase Is Part of the Virion 616 Micro Focus:
27.7 Retroviruses: Plus-Strand Viruses Embrace Your Gut Flora, for You Know
That Use Reverse Transcriptase in Their Not What They Do 685
Life Cycles 618 32.1 Many Types of Microbial Interactions
27.8 Reverse Transcribing DNA Viruses 619 Exist 686
Microbial Diversity & Ecology 32.1
Wolbachia pipientis: The World’s Most
Part Six Ecology and Symbiosis Infectious Microbe? 687
32.2 The Human-Microbe Ecosystem 698
28 Biogeochemical Cycling and Global Climate Microbial Diversity & Ecology 32.2
Change 623 Do Bacteria Make People Fat? 700
Micro Focus: 32.3 Normal Microbiota of the Human Body
Global Climate Change; Global Adapt to the Human Condition 700
Infectious Disease Change? 623
28.1 Biogeochemical Cycling Sustains Life
on Earth 624 Part Seven Pathogenicity and Host Response
28.2 Global Climate Change: Biogeochemical
Cycling Out of Balance 633 33 Innate Host Resistance 707
29 Methods in Microbial Ecology 637 Micro Focus: Supersize Me! 707
33.1 Immunity Arises from Innate Resistance
Micro Focus:
and Adaptive Defenses 707
Scientists Search for Intraterrestrial
33.2 Innate Resistance Starts with Barriers 708
Life—and Find It 637
33.3 Innate Resistance Relies on Chemical
29.1 Microbial Biology Relies on Cultures 638 Mediators 712
29.2 Genetic Methods Are Used to Assess 33.4 Cells, Tissues, and Organs Work
Microbial Diversity 641 Collectively to Form an Immune System 717
29.3 Assessment of Microbial Community 33.5 Phagocytosis: Destroying Invaders and
Activity Relies on Biochemistry and Recycling Their Parts 726
Genetics 645 33.6 Inflammation Unites All the Components
30 Microorganisms in Marine and Freshwater of Immunity 731
Ecosystems 650
34 Adaptive Immunity 736
Micro Focus:
Ocean Death Coming Soon to a Coast Micro Focus: It’s in My Genes? 736
Near you 650 34.1 Adaptive Immunity Relies on Recognition
30.1 Water Is the Largest Microbial Habitat 651 and Memory 736
30.2 Microorganisms in Marine Ecosystems 652 34.2 Molecules That Elicit Immunity Are Called
30.3 Microorganisms in Freshwater Ecosystems 661 Antigens 738
34.3 Adaptive Immunity Can Be Earned or
31 Microorganisms in Terrestrial Ecosystems 667 Borrowed 739
Micro Focus: A Short History of Rust 667 34.4 Recognition of Foreignness Is Critical for
31.1 Soils Are an Important Microbial Habitat 667 a Strong Defense 740

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34.5 T Cells Oversee and Participate in 37.2 Epidemiology Is Rooted in Well-Tested

Immune Functions 743 Methods 808
34.6 B Cells Make Antibodies and Do a Historical Highlights 37.3
Whole Lot More 747 A Modern Epidemic Exposed 809
34.7 Antibodies Are Proteins That Bind 37.3 Infectious Disease Is Revealed Through
to Specific 3-D Molecules 749 Patterns Within a Population 812
34.8 Antibody Binding Dooms the Target 757
Historical Highlights 37.4
Techniques & Applications 34.1 “Typhoid Mary” 814
Monoclonal Antibody Therapy 758
37.4 Infectious Diseases and Pathogens
34.9 Not Responding Is Also Part of Immunity 760 Are Emerging and Reemerging 815
34.10 Sometimes the Immune System 37.5 Health-Care Facilities Harbor Infectious
Doesn’t Work the Way It Should 760 Agents 816
37.6 Coordinated Efforts Are Required to
35 Pathogenicity and Infection 770 Prevent and Control Epidemics 818
Micro Focus: Sneaky Little Buggers 770 Historical Highlights 37.5
35.1 Pathogenicity Drives Infectious Disease 770 The First Immunizations 820
35.2 Virulence Defines a Pathogen’s Success 773 37.7 Bioterrorism Readiness Is an Integral
35.3 Exposure and Transmission Can Lead to Component of Public Health Microbiology 822
Infectious Disease 782
Historical Highlights 37.6
Historical Highlights 35.1 1346—The First Recorded Biological
The First Indications of Person-to-Person Warfare Attack 823
Spread of an Infectious Disease 783
38 Human Diseases Caused by Viruses
and Prions 827
Part Eight  Microbial Diseases, Detection, Micro Focus:
and Their Control Honest . . . It Was the Mosquito! 827
36 Clinical Microbiology and Immunology 786 38.1 Viruses Can Be Transmitted by Airborne
Routes 828
Micro Focus: Seeing the Next Frontier 786
38.2 Arthropods Can Transmit Viral Diseases 836
36.1 The Clinical Microbiology Laboratory
38.3 Direct Contact Diseases Can Be
Is the Front Line for Infectious Disease
Caused by Viruses 837
Detection 786
38.4 Food and Water Are Vehicles for
36.2 Biosafety Practices Protect Lab Workers 787
Viral Diseases 851
36.3 Identification of Microorganisms from
Historical Highlights 38.1
Specimens 790
A Brief History of Polio 853
36.4 Immune Responses Can Be Measured or
Exploited to Detect Infections 797 38.5 Zoonotic Diseases Arise from
Human-Animal Interactions 854
37 Epidemiology and Public Health Microbiology 806 38.6 Prion Proteins Transmit Disease 856
Micro Focus: Practice What You Preach 806
39 Human Diseases Caused by Bacteria 859
37.1 Epidemiology Is an Evidence-Based
Science 806 Micro Focus:
Historical Highlights 37.1 “This Little Piggie Stayed Home” 859
The Birth of Public Health in the 39.1 Bacteria Can Be Transmitted by
United States 807 Airborne Routes 859
Historical Highlights 37.2 39.2 Arthropods Can Transmit Bacterial
John Snow, the First Epidemiologist 808 Diseases 868

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39.3 Direct Contact Diseases Can Be 41.4 Detection of Food-Borne Pathogens

Caused by Bacteria 872 Requires Government-Industry Cooperation 936
Disease 39.1 41.5 Microbiology of Fermented Foods: Beer,
A Brief History of Syphilis 879 Cheese, and Much More 937
Disease 39.2 Techniques & Applications 41.1
Biofilms 880 Chocolate: The Sweet Side of Fermentation 938
39.4 Food and Water Are Vehicles for Bacterial 41.6 Probiotics 944
Diseases 885
Techniques & Applications 39.3 42 Biotechnology and Industrial Microbiology 947
Clostridial Toxins as Therapeutic Agents: Micro Focus:
Benefits of Nature’s Most Toxic Proteins 889 Where Are the New Antibiotics? 947
39.5 Zoonotic Diseases Arise from 42.1 Microbes Are the Source of Many
Human-Animal Interactions 894 Products of Industrial Importance 948
39.6 Opportunistic Diseases Can Be Caused 42.2 Biofuel Production Is a Dynamic Field 950
by Bacteria 897 42.3 Growing Microbes in Industrial Settings
Presents Challenges 951
40 Human Diseases Caused by Fungi 42.4 Production Strains Are Developed
and Protists 902 to Maximize Output of Industrially
Micro Focus: Death by—Mushroom? 902 Important Compounds 953
40.1 Relatively Few Fungi and Protists 42.5 Agricultural Biotechnology Relies on
Are Human Pathogens 902 a Plant Pathogen 959
40.2 Fungi and Protists Can Be Transmitted 42.6 Some Microbes Are Products 959
by Airborne Routes 904
43 Applied Environmental Microbiology 964
Disease 40.1
A Brief History of Malaria 907 Micro Focus:
40.3 Arthropods Can Transmit Fungal and Deepwater Horizon Oil Consumed
Protozoal Disease 907 by Microbes 964
40.4 Direct Contact Diseases Can Be Caused 43.1 Purification and Sanitary Analysis
by Fungi and Protists 914 Ensure Safe Drinking Water 964
40.5 Food and Water Are Vehicles of Fungal 43.2 Wastewater Treatment Maintains
and Protozoal Diseases 917 Human and Environmental Health 968
40.6 Opportunistic Diseases Can Be Caused 43.3 Microbial Fuel Cells: Batteries
by Fungi and Protists 921 Powered by Microbes 975
43.4 Biodegradation and Bioremediation
Harness Microbes to Clean the
Environment 976
Part Nine Applied Microbiology
41 Microbiology of Food 927 Appendix 1  Review of the Chemistry of
A
Biological Molecules A-1
Micro Focus:
The Art, Science, and Genetics of Appendix 2 Common Metabolic Pathways A-9
Brewing Beer 927
41.1 Microbial Growth Can Cause Food Appendix 3 Microorganism Pronunciation Guide A-17
Spoilage 928
41.2 Various Methods Are Used to Control Glossary G-1
Food Spoilage 930 Credits C-1
41.3 Food-Borne Disease Outbreaks 933 Index I-1

xxii
 1
The Evolution
of Microorganisms
and Microbiology
Over 4,000 Potential Planets Discovered
A s of July 2015, the National Aeronautics and Space Administration
(NASA) reported that over 4,000 potential planets and almost 1,000
confirmed planets had been discovered by the 2009 Kepler mission. Using
a telescope in space, the light emanating from stars as far as 3,000 light-
years away had been monitored every half-hour. The Kepler telescope
identified planets as they circulated their star and caused a brief decrease
in emitted light; just as an object is detected as a blip by radar, a blip of
“darkness” indicates a possible planet.
Unless you are a science fiction fan, you might wonder why NASA
is interested in finding planets. By finding other planets, scientists can
gather evidence to support or refute current models of planet formation.
These models predict a process that is chaotic and violent. Planets are
thought to begin as dust particles circling around newly formed stars.
As these particles collide, they grow in size, forming larger chunks.
Eventually a series of such collisions results in planet-sized bodies.
NASA astrobiologists are interested in identifying characteristics of a
planet that may allow it to support life. Using Earth as a model, they
hypothesize that life-supporting planets will share many features with
Earth. But how will life be recognized? Scientists look to life on Earth
to answer this question, and increasingly they are turning to micro­
biologists for help.
Earth formed 4.5 billion years ago. Within the next billion years, the first
cellular life forms—microbes—appeared. Since that time, microorganisms
have evolved and diversified to occupy virtually every habitat on Earth: from
oceanic geothermal vents to the coldest Arctic ice. The diversity of cellular
microorganisms is best exemplified by their metabolic capabilities. Some
carry out respiration, just as animals do. Others perform photosynthesis,
rivaling plants in the amount of carbon dioxide they capture, forming
organic matter and releasing oxygen into the atmosphere. Still other
microbes are able to use inorganic molecules as sources of energy in both
Artist’s rendition of the six planets orbiting a star called Kepler-11.
The drawing is based on observations made of the system by the
Kepler spacecraft on August 26, 2010. Some are Earth-sized and
may be habitable by life.
oxic (oxygen available) and anoxic (no oxygen) conditions. Microbes also
are diverse in terms of environmental conditions. Some withstand
extremes of temperature, pressure, and pH. Indeed, studies have shown
that some Earth microbes tolerate conditions that simulate those on Mars.
These microbes are important for understanding what life might be like
on other worlds.
Our goal in this chapter is to introduce you to the amazing world of
microorganisms and to outline the history of their evolution and discovery.
Microbiology is a biological science, and as such, much of what you will learn in
this text is similar to what you have learned in high school and college biology
classes that focus on large organisms. But microbes have unique properties,
so microbiology has unique approaches to understanding them. These too will
be introduced. But before you delve into this chapter, check to see if you have
the background needed to get the most from it.
Readiness Check:
Based on what you have learned previously, you should be able to:
✔ List the features of eukaryotic cells that distinguish them from other
cell types
✔ List the attributes that scientists use to determine if an object is alive
1.1 Members of the Microbial World
After reading this section, you should be able to:
■ Differentiate the biological entities studied by microbiologists from
those studied by other biologists
■ Explain Carl Woese’s contributions in establishing the three-domain
system for classifying cellular life
■ Provide an example of the importance to humans of each of the
major types of microbes
■ Determine the type of microbe (e.g., bacterium, fungus, etc.) when
given a description of a newly discovered microbe
1
2 CHAPTER 1 | The Evolution of Microorganisms and Microbiology

Organisms and
biological entities
studied by
microbiologists

can be

Cellular Acellular

includes includes

Fungi Protists Bacteria Archaea Viruses Viroids Satellites Prions

e.g. e.g. e.g. e.g. composed of composed of composed of composed of

Yeasts Algae Escherichia Methanogens Protein and Nucleic acid

RNA Protein
Molds Protozoa coli nucleic acid enclosed in a
Slime molds protein shell

Figure 1.1 Concept Map Showing the Types of Biological Entities Studied by Microbiologists.
MICRO INQUIRY How would you alter this concept map so that it also distinguishes cellular organisms from each other?

Microorganisms are defined as those organisms too small to be
seen clearly by the unaided eye (figure 1.1). They are generally
1 millimeter or less in diameter. Although small size is an im-
portant characteristic of microbes, it alone is not sufficient to
define them. Some microbes, such as bread molds and filamen-
tous photosynthetic microbes, are actually visible without mi-
croscopes. These macroscopic microbes are often colonial,
consisting of small aggregations of cells. Some macroscopic
microorganisms are multicellular. They are distinguished from
other multicellular life forms such as plants and animals by their
lack of highly differentiated tissues. Most unicellular microbes
are microscopic. However, there are interesting exceptions, as
we describe in chapter 3. In summary, cellular microbes are
usually smaller than 1 millimeter in diameter, often unicellular
and, if multicellular, lack differentiated tissues.
In addition to microorganisms, microbiologists study a va-
riety of acellular biological entities (figure 1.1). These include
viruses and subviral agents. Although the term “microorganism”
is often applied only to cellular microbes, some texts use both
“microorganism” and “microbe” when referring to these acel-
lular agents.
The diversity of microorganisms has always presented a
challenge to microbial taxonomists. The early descriptions of
cellular microbes as either plants or animals were too simple.
For instance, some microbes are motile like animals but also
have cell walls and are photosynthetic like plants. Such mi-
crobes cannot be placed ­easily into either kingdom. An impor-
tant breakthrough in microbial taxonomy arose from studies
of their cellular architecture, when it was discovered that cells
exhibited one of two possible “floor plans.” Cells that came to
be called prokaryotic cells (Greek pro, before, and karyon, nut
or kernel; organisms with a primordial nucleus) have an open
floor plan. That is, their contents are not divided into compart-
ments (“rooms”) by membranes. The most obvious character-
istic of these cells is that they lack the membrane-delimited
nucleus observed in eukaryotic cells (Greek eu, true, and karyon,
nut or kernel). Eukaryotic cells not only have a nucleus but also
many other membrane-bound organelles that separate some
cellular materials and processes from others.
These observations eventually led to the development of a
classification scheme that divided organisms into five kingdoms:
Monera, Protista, Fungi, Animalia, and Plantae. Microorganisms
(except for viruses and other acellular infectious agents, which
have their own classification system) were placed in the first three
kingdoms. In this scheme, all organisms with prokaryotic cell
structure were placed in Monera. The five-kingdom system was an
important development in microbial taxonomy, but it is no longer
accepted by microbiologists. This is because not all “prokaryotes”
are the same and therefore should not be grouped together in a
single kingdom. Furthermore, it is currently argued that the term
prokaryote is not meaningful and should be abandoned. As we
describe next, this discovery required several advances in the
tools used to study microbes. Use of the term “prokaryote”
is controversial (section 3.1)
Great progress has been made in three areas that profoundly
affect microbial classification. First, much has been learned
about the detailed structure of microbial cells from the use of
electron microscopy. Second, microbiologists have determined
Another random document with
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after hunting an enormous male elephant for five hours, they had at
length brought him to a stand, near Bree, about ten miles north-east
of Kouka. Mr. Toole and myself instantly mounted our horses, and,
accompanied by a Shouaa guide, we arrived at the spot where he
had fallen, just as he breathed his last.
Although not more than twenty-five years old, his tusk measuring
barely four feet six inches, he was an immense fellow. His
dimensions were as under:
ft. in.
Length from the proboscis to the tail 25 6
Proboscis 7 6
Small teeth 2 10
Foot longitudinally 1 7
Eye 2 by 1½
From the foot to the hip-bone 9 6
From the hip-bone to the back 3 0
Ear 2 by 2 6
I had seen much larger elephants than this alive, when on my last
expedition to the Tchad; some I should have guessed sixteen feet in
height, and with a tusk probably exceeding six feet in length. The
one before me, which was the first I had seen dead, was, however,
considered as of more than common bulk and stature; and it was not
until the Kanemboo of the town of Bree came out, and by attracting
his attention with their yells, and teasing him by hurling spears at his
more tender parts, that the Shouaas dared to dismount; when, by
ham-stringing the poor animal, they brought him to the ground, and
eventually despatched him by repeated wounds in the abdomen and
proboscis: five leaden balls had struck him about the haunches, in
the course of the chase, but they had merely penetrated a few
inches into his flesh, and appeared to give him but little uneasiness.
The whole of the next day the road, leading to the spot where he lay,
was like a fair, from the numbers who repaired thither for the sake of
bringing off a part of the flesh, which is esteemed by all, and even
eaten in secret by the first people about the sheikh: it looks coarse,
but is better flavoured than any beef I found in the country. Whole
families put themselves in motion, with their daughters mounted on
bullocks, on this occasion, who, at least, hoped as much would fall to
their share as would anoint their heads and persons plentifully with
grease at the approaching fsug. The eyes of this noble animal were,
though so extremely small in proportion to his body, languid and
expressive even in death. His head, which was brought to the town, I
had an opportunity of seeing the next day, when I had it opened; and
the smallness of the brain is a direct contradiction to the hypothesis,
that the size of this organ is in proportion to the sagaciousness of the
animal. His skin was a full inch and a half in thickness, and dark
gray, or nearly black, hard, and wrinkled: his ears, large and
hanging, appeared to me the most extraordinary part about him,
particularly from the facility with which he moved them backwards
and forwards: his feet are round, undivided, and have four nails, or
hoofs, for they cannot be called toes, two in the front of the foot,
about an inch in depth, and two inches in length, which join each
other, with two smaller ones on each side of the foot. In Africa they
are scarcely ever taken alive, but hunted as a sport, for the sake of
their flesh; and also in order to obtain their teeth, which, however, as
they are generally small, are sold to the merchants for a very trifling
profit. The manner of hunting the elephant is simply this: from ten to
twenty horsemen single out one of these ponderous animals, and,
separating him from the flock by screaming and hallooing, force him
to fly with all his speed; after wounding him under the tail, if they can
there place a spear, the animal becomes enraged. One horseman
then rides in front, whom he pursues with earnestness and fury,
regardless of those who press on his rear, notwithstanding the
wounds they inflict on him. He is seldom drawn from this first object
of his pursuit; and, at last, wearied and transfixed with spears, his
blood deluging the ground, he breathes his last under the knife of
some more venturesome hunter than the rest, who buries his dagger
in the vulnerable part near the abdomen: for this purpose he will
creep between the animal’s hinder legs, and apparently expose
himself to the greatest danger: when this cannot be accomplished,
one or two will ham-string him, while he is baited in the front; and this
giant of quadrupeds then becomes comparatively an easy prey to his
persecutors.
Jan. 12.—Karouash came to us this evening, with his dark Arab
eyes, sparkling with somewhat more than vivacity; and it was not
long before we found out the cause. The people of Gulphi, who
inhabited a town close to the banks of the Shary, had no other
means of raising their grain (the land surrounding their walls being all
tributary to the sheikh) than by planting it on the south bank of that
river; reaping in the season, and carrying the produce to their city by
means of their flat-bottomed boats. They had, of late, been so little
interrupted in their agricultural pursuits, by the boats of the
neighbouring towns, that a village of huts had sprung up on this
portion of land; and labourers, to the number of three or four
hundred, resided there constantly. The hostile movements of the
Begharmis had, however, made the sheikh’s people more on the
alert than formerly; and passing over the river in their own boats,
accompanied by several deserters from Gulphi, who, traitor-like,
consented to bear arms against the land that gave them birth, and
lead its enemies to the pillage of their brethren, the people of
Maffatai and Kussery had, a few nights before, made an attack on
this village, putting to death all the males, even while they slept; and,
as usual, dragging the women and children to their boats, returned to
their homes without the loss of a man, after setting fire to all the huts,
and more than four hundred stacks of wheat and gussub. The effects
produced by this midnight expedition, and which was celebrated by
singings and rejoicings throughout Kouka, were indeed of a nature
favourable to my prospects, notwithstanding the shock humanity
received from the cause. The Begharmis, who had occupied the
southern banks of the Shary for months, obliging even the Loggun
people to supply them with provisions, took such alarm at this attack
of the sheikh’s people, that they struck their camp, and retired
immediately on the news reaching them; and the Loggun nation as
quickly sent off to the sheikh a deputation, with sixty slaves, and
three hundred bullocks, congratulating him on the event.
I determined on making immediate application for permission to
visit this country; so full of interest, both from its situation, and the
waters by which it was reported to be bounded. No time was to be
lost, for the return of the enemy might be as sudden as his flight; and
again I might have my intentions frustrated. I had been eleven
months endeavouring to visit this country—but to climb steep hills
requires a slow pace at first.
Jan. 18.—The sheikh, who had never, on any one occasion,
neglected making every possible arrangement for carrying my
wishes into execution, had not only instantly complied with my
request to seize this opportunity of visiting Loggun, but sent this
morning Karouash to advise with me as to my proceedings, and to
recommend my going without loss of time. “Bellal shall go with you,”
said he; “who has been in my confidence for seventeen years, and to
whom I could trust my own life, or that of my children, who are even
dearer to me than life itself.”
But in the morning we found a brown horse, which had carried Mr.
Toole from Tripoli, dead within our inclosure: both this and a black
one, which his Arab had been mounted on by the bashaw, had
scarcely eaten any thing since their arrival here. Our departure was
therefore put off for this day. Troubles, however, never come alone.
In the evening the camels I intended to take with me were missing;
and although the people were out looking for them until midnight, we
had no tidings. In the night I was called up, as Mr. Toole’s other
horse was dying: no blood could be got from him; and after
staggering about, in a way resembling intoxication, he died before
daylight.
Jan. 22.—Karouash, Ben Taleb, and even the sheikh, now
exclaiming against our going out, “Wonderful! Wonderful!” said they,
“it is written you are not to go.” The delay perplexed me, although to
go, and quickly, I was determined; the time was precious, for I did
not wish the news of my intentions to precede me. Towards night my
camels were found; and the sheikh, hearing that we had been
inquiring for a horse to purchase, sent a very smart black galloway to
Mr. Toole as a present. We had now seen die on our hands, in the
space of nine months, thirty-three camels, six horses, and one mule.
 On the 23d I intended being off by daylight; but it was the
afternoon before I could accomplish my wish. The sheikh had given
me Bellal: “He will obey your orders in every thing,” said he; “but you
are going amongst people with whom I have but little influence.”
Bellal, who was one of the handsomest negroes I almost ever saw,
and a superior person, was attended by six of his slaves, two of
whom were mounted; these, with ourselves and two camels, formed
our party. While I was waiting to take leave of the sheikh, a note was
brought me from Dr. Oudney, by a Bornouese from Katagum: it had
no date, and was indeed his last effort. The acknowledgment of
being weak and helpless assured me that he was really so; for
during the whole of his long sufferings a complaint had scarcely ever
escaped his lips. On the sheikh’s saying to him, when he first
expressed his wish to accompany the kafila, “Surely your health is
not such as to risk such a journey?” he merely replied, “Why, if I stay
here, I shall die, and probably sooner, as travelling always improves
my health.”
His letter, though short, expresses great satisfaction at the
treatment he had met with on his journey, and also from the
inhabitants of the country.
 FOOTNOTES:

[34]The most beautiful Jewess in Tripoli is called Mesrouda-

eyum el Oubara (Mesrouda, with the eye of the Oubara).
[35]The anniversary of Abraham’s offering up Isaac, or the
meeting of Pilgrims at Mecca.
[36]Strips of cotton, so many fathoms of which go to a dollar.
[37]Abyssinian hornbill.
[38]In Tripoli, the father or mother is generally the executioner,
to avenge the sin, and at the same time wipe the stain from the
family, and prevent public execution.
[39]Marry her.
[40]The horn of one of these animals measured two feet, six
inches, and three-quarters, in circumference.
[41]On these occasions the sheikh merely moves his finger,
which is the signal for immediate execution.
 [42]Black Mameluke.
[43]A religious mendicant: the name is nearly the Arabic for
poverty.
[44]Soon after this, I made an offer to two Arabs, both of whom
had formerly been at Waday, that I would give them each two
hundred dollars, if they would accompany me: this is a sum for
which an Arab will almost do any thing; but they refused, saying
“No! no! what is money without life? the Waday people will kill us
all.”
[45]Governor of the palace.
[46]A town near Mesurata.
 CHAPTER VI.
EXCURSION TO LOGGUN, AND DEATH OF MR. TOOLE.

Jan. 1824.—We passed the night of the 24th at Angornou, and

proceeded, without leaving the lake at any great distance, for two
days, when we arrived at Angala, one of the ancient governments
subject to Bornou. The present sultan was the first friend and
supporter of El Kanemy; and, twenty-five years ago, when he was
only a merchant, betrothed to him his daughter Miram in marriage,
with a large dower in slaves and cattle. The sultan, a most
benevolent-looking old black, received us with great kindness and
hospitality; and as soon as we were lodged in the house of the
delatoo (prime minister), bowls of milk, rice, flour, and honey, were
brought to us; an abundance of eatables were also sent in the
evening, and the next morning a very fine live sheep.
Miram (princess in the Bornou language), now the divorced wife
of the sheikh El Kanemy, was residing at Angala, and I requested
permission to visit her. Her father had built for her a very fine house,
in which she constantly resided: her establishment exceeded sixty
persons. She was a very handsome, beautifully formed negress, of
about thirty-five, and had imbibed much of that softness of manner
which is so extremely prepossessing in the sheikh. Seated on an
earthen throne, covered with a turkey carpet, and surrounded by
twenty of her favourite slaves, all dressed alike, in fine white shirts,
which reached to their feet, their necks, ears, and noses thickly
ornamented with coral; she held her audience with very considerable
grace, while four eunuchs guarded the entrance; and a negro dwarf,
who measured three feet all but an inch, the keeper of her keys, sat
before her with the insignia of office on his shoulder, and richly
dressed in Soudan tobes. This little person afforded us a subject of
conversation, and much laughter. Miram inquired whether we had
such little fellows in my country, and when I answered in the
affirmative, she said, “Ah gieb! what are they good for? do they ever
have children?” I answered “Yes; that we had instances of their
being fathers to tall and proper men.” “Oh, wonderful!” she replied: “I
thought so; they must be better then than this dog of mine; for I have
given him eight of my handsomest and youngest slaves, but it is all
to no purpose. I would give a hundred bullocks, and twenty slaves, to
the woman who would bear this wretch a child.” The wretch, and an
ugly wretch he was, shook his large head, grinned, and slobbered
copiously from his extensive mouth, at this flattering proof of his
mistress’s partiality.
We left Angala the following day, to the great distress of our host,
the delatoo, who would have feasted us for a week. A child had been
borne by one of his wives, just about the time Dr. Oudney had
passed through on his visit to Showy; which, in return for his
prescriptions, the delatoo had named Tibeeb, the Doctor’s travelling
name. Indeed, there was a liberality of feeling and toleration about
our host deserving most honourable mention; and when, on my
return from Loggun, worn out by fatigue and anxiety, I really required
nursing, he introduced his sister, a female of most matronly
deportment, who superintended the process of shampooing, which
was performed by one of her best looking and most accomplished
handmaids. On my expressing my thanks to the delatoo for these
unlooked-for attentions, he replied, “It grieved us all to see so great a
man as yourself, so far from home, a stranger and without women;
when in your own country, ‘gray hairs to you!’ you have, at least, a
hundred, I dare say!”
On the 23d we reached Showy, on the banks of the river Shary:
the magnitude of the stream drew from us both an involuntary
exclamation of surprise; it appeared to be full half a mile in width,
running at the rate of two to three[47] miles an hour, in the direction
nearly of north. In the centre of the river is a beautiful island, nearly a
mile in length, in front of the town. Showy forms part of the district of
Maffatai, and is governed by a kaid: and this person, who treated us
with great attention, proposed that we should proceed down the
stream to the Tchad, according to the sheikh’s directions.
On the 2d of February we embarked, accompanied by the kaid
and eight canoes, carrying ten and eleven men each: ploughing the
stream with their paddles, for nearly eight hours, they brought us, by
sunset, to a spot called Joggabah (or island, in the Mekkari
language), about thirty-five miles from Showy. The river, full as it is of
water at this season, had a highly interesting appearance: one noble
reach succeeded another, alternately varying their courses by
handsome sweeps, some of them three and four miles in length; the
banks were thickly scattered with trees rich in foliage, and all hung
over with creeping plants, bearing various coloured and aromatic
blossoms, amongst which the purple convolvolus flourished in great
beauty: several crocodiles, from eight to fifteen feet in length, were
slumbering on the banks, which, on our near approach, rolled into
the stream, and disappeared in an instant. The natives appeared to
fear them but little in shallow water, but dived in with great boldness
after the ducks we shot, and a large iguana that we struck while
sleeping on a tamarind tree, and which fell headlong into the river.
Joggabah is a beautiful feature in the scenery, as well as a
prominent one; and is seen for nearly six miles in proceeding down a
very wide, handsome reach, which we called Belle-vue Reach. The
river is here quite as wide as at Showy, which, with this exception, I
take to be the widest part.
Drawn by Captn. Clapperton. Engraved by E. Finden.

FISHING BOATS ON THE SHARY.

Published Feb. 1826, by John Murray, London.

This island is high ground, with steep and nearly perpendicular

banks, and a depth of ten feet water close to the edge: the canoes
moor up to the shore; the stream runs strong and clear; and the
landing is on a fine dry sandy beach: it extends to the Tchad north, a
distance of twelve or fifteen miles, and has two handsome streams
bounding it, which run north-east and north-west, and by which the
Shary takes its way into that immense lake. It abounds with game:
and we had fish in abundance, venison, the flesh of a buffalo, and
wild ducks, for supper, all roasted on wooden spits.
 We pitched our tent on the jutting head, where, a few years ago,
stood a negro town: the inhabitants, however, were refractory,
committed piracies on the Showy people, and in consequence the
sheikh determined on exterminating them. They were in league with
the Biddoomah, who were now kept to their own islands. Joggabah
we found uninhabited, and covered with jungle and prickly
underwood, in that part where we passed the night: we saw thirty
porcupines, and killed a centipede and two scorpions under our
mats. We had two canoes rowing guard the whole night on account
of the Biddoomah. By daylight we re-embarked, and proceeded by
the north-west branch for more than two hours, keeping nearly the
same direction: we passed several marshy floating islands, covered
with rushes, high grass, and papyrus, apparently dividing the water
into different streams, when we found ourselves in that sea of fresh
water, the Tchad, which we named Lake Waterloo, and into which
the Shary empties itself. It was my intention to have proceeded quite
round the island to the east, and to have returned by the other
branch; but after making about two miles in the open lake, a heavy
swell from the north-east caused so much water to come into the
canoes, and so much labour to the men, that we gave up that idea.
After our return to the south side of the island we followed the north-
east branch, and found it vary but little in appearance. During our
passage, by keeping the deepest water, and avoiding the convexities
of the stream, we, at this season, met with no impediments; and had
nowhere less than three feet water. We passed many small islands,
all of which, near the mouth, were destitute of trees, but covered with
reeds (among which was the papyrus), bamboos, and very tall
grasses: the quantity of water-fowl was immense, of great variety,
and beautiful plumage. The nearest Biddoomah island is said to be
three days voyage on the open lake, from the mouth of the river, in a
north-east direction, say ninety miles, during two of which these
canoes lose sight of land: with an excellent telescope I could discern
nothing but the waste of waters to the north or east. The Biddoomah
are a wild and independent people, who carry on a piratical war with
all their neighbours: they send out fleets of sixty or one hundred
canoes; and they are reported as terrible kaffirs.
 We now commenced our return, and a laborious business it was,
rowing or paddling against the stream: the paddles were only
resorted to when, now and then, a headland sheltered them from the
wind and current; and so cautious were the men of Showy, that it
was near midnight before we landed on a spot named Buffalo Bank.
We had endured two days of burning heat and exposure to the sun,
and a night of watchfulness and torture from the insects; added to
this, we had lived entirely on Indian corn, boiled in the canoes during
the day: we were also constantly ankle deep in water, from the
leaking of the canoes. The banks were here, for some miles inland,
thickly clothed with handsome trees encompassed by creeping
shrubs in full blossom, while large antelopes and buffaloes were
starting from the thickets where they had fixed their lairs. We
disturbed a flock of several buffaloes on our making the shore; and
hippopotami came so close to us as to be struck by the paddles:
here, and at the confluence of the two branches, we found the
greatest depth of water. The most desirable route for us now to have
pursued would have been to have gone from hence to Loggun by
water, but Gulphi lay in our way, and it was impossible. To follow the
direction of the river, therefore, as nearly as we could, by moving in a
line parallel to its banks, became our next anxiety.
Previously, however, we again embarked, and visited a spot
called Dugheia, within a day’s journey of Gulphi, higher up the
stream. Dugheia is a ford and a ferry, where the sheikh, with all his
people, pass the stream on their expeditions against the Begharmis:
the ford is in a slanting direction, and between two sinuosities. When
the river is at its greatest height, the water reaches up to the neck; it
was now not above the arm-pits of a good sized man. The infantry,
placing their spears and bags of corn on their heads, in their shields,
cross with ease: the cavalry are moved over in canoes, and the
horses swam at the sterns. The appearance of the river is similar
both above and below Showy: excepting that above there are more
picturesque islands; on one of which we passed the night, and
named it Red Heron Isle, as my poor friend shot there a bird of that
species.
 On the 8th of February we returned to Showy, and the day
following pursued our route by Willighi and Affadai. Willighi is a
walled town of considerable strength; indeed the Begharmis always
pass it by on their predatory excursions. The walls are nearly fifty
feet high, with watch-towers erected on the salient angles, where
there are constant sentinels. The sultan also lives in a sort of citadel
with double walls, and three heavy gates in each wall, strongly
bound with iron. Borgomanda, the reigning sultan of Begharmi, and
Cheromah (which means heir-apparent), send annual presents to
Mai Dundelmah, the sultan of Willighi; but he is a hadgi, and holds
the sheikh of Bornou in too high estimation to forsake his fortunes.
Before arriving at Willighi, which is only a day’s journey from Gulphi,
we recrossed the Gurdya, a considerable stream running from the
Shary into the great lake.
Feb. 10.—We left Willighi, after presenting the sultan with two
knives, two pairs of scissors, a turban, and a red cap, and in about
two hours arrived at another ford of the water Maffatai. These fords
are known by the natives of the neighbouring towns only, who are
always hired as guides. The water was up to the body of the horse;
and a weak camel, by encountering the load of another, was thrown
off the causeway into twelve or fourteen feet of water. We crossed,
this day, three deep marshes, besides the river, which, the Willighi
guide informed us, extended to the river, at one of which we were
detained nearly an hour before we could venture a passage: the
water reached to our saddles. After the rainy season, canoes come
from Showy to the neighbourhood of Willighi, for a wood which is
here abundant, called by the natives kagam, and another called
korna, with which they build their canoes, and make their paddles.
The fruit, also, of a species of locust tree, which the natives call
kadellaboo, is here gathered. We rested under the shade of a
beautiful large tree of this description, bearing a flower of a deep
crimson colour; a yellow jessamine, with a delicious odour, was
creeping around it, while other delicate aromatic plants grew in wild
profusion. Nevertheless, the paths through these woods, though
literally strewed with flowers, were nearly impassable from the
overhanging branches of thorny shrubs, which not only tore our
shirts and cloaks, but were sufficiently strong to drag the loads from
the backs of the camels: we were nearly twelve hours in making
twenty-two miles. When we arrived at the town of Affadai, our people
were too tired to cook the rice we had with us, and the kadi merely
sent us flour and water paste, and leban (sour milk): at the same
time promising to kill a sheep the next day, if we would stay. We,
however, departed early on the following morning, and came,
towards evening, to a place called Kala, a wretched nest of huts,
although surrounded by a wall, and having strong gates.
On the 12th we moved on, and, after crossing a long and deep
marsh, we halted, about noon, for an hour or two, at a town called
Alph, which stood on a foundation of earth artificially raised in the
midst of a swamp extending for miles in every direction. We shot
several cranes; one of a beautiful white, with a yellow beak, and dark
hazel eyes, with a yellow rim. We now began to approach Kussery,
and again came to the banks of the river Shary, leaving Gulphi to the
eastward. This route is but seldom traversed: it is a continued
succession of marshes, swamps, and stagnant waters, abounding
with useless and rank vegetation: flies, bees, and mosquitos, with
immense black toads, vie with each other in a display of their peace-
destroying powers.
I had, with grief, for several days, observed in my companion
symptoms which gave me great uneasiness: his stomach constantly
refused our coarse food of fish and paste; but as he complained but
little, I hoped a day or two at Kussery would restore his wonted good
health and spirits. Kussery, however, unfortunately, was the last
place one should have chosen for rest and tranquillity: during several
hours in the day, the inhabitants themselves dare not move out, on
account of the flies and bees. The formation of the houses, which
are literally one cell within another, five or six in number, excited my
surprise; which was not a little increased when I found that they were
built expressly as a retreat from the attacks of these insects. Still I
was incredulous, until one of our people, who had carelessly gone
out, returned with his eyes and head in such a state, that he was
extremely ill for three days. Kussery is a strong walled town,
governed by an independent sultan, named Zarmawha, who has
twice been in rebellion against the sheikh. Bellal was obliged to take
off his red cap and turban, and enter the presence with his head and
feet bare—a ceremony which had previously been dispensed with on
our journey. The sultan merely peeped at us through a lattice-work of
bamboo, but inquired particularly, why I turned my face towards him
as I sat. I, of course, replied, that turning my back would be, in my
country, a gross affront; at which he laughed heartily. We had a
separate letter to this prince from the sheikh: he seemed, however,
to pay but little respect to it, or the bearer, Bellal, while to me he was
most attentive. We had ten dishes of fish and paste, which regaled
our attendants sumptuously; and one of his own household took up
his residence at our huts. The fish was stale, and offensive to more
senses than one, which the natives rather prefer, as we do game
that has hung some time. The sultan’s officer, however, seeing that I
could not touch these Kussery delicacies, quickly brought me a mess
made of fresh fish, which, though a little oily, was not unpalatable,
with a large bowl of leban. Salt is here scarcely known, and therefore
not eaten with any of their meals: out of the small stock I had
brought, the townspeople were always begging little lumps, which
they put into their mouths, and sucked with as much satisfaction as if
it had been barley sugar.
I gave the sultan, in the morning, a parcel of beads, two pairs of
scissors, a knife, two turkadees, and a turban; on which he said “we
were a great people, a race of sultans, and would bring good fortune
to his dominions!” I must not omit to mention a visit which I received
from the sultan’s sister. She had been some time divorced from her
husband, who had gone over to the Begharmis. The officer in
attendance on us announced her with great secrecy, about ten
o’clock at night. For the only light in our hut we were indebted to the
pale moonbeams which shone through the door-way, as we had
neither candles nor lamp; and I had been some time fast asleep
when she arrived. Her attendants, three in number, waited for her at
the entrance, while she advanced and sat herself down beside my
mat: she talked away at a great rate, in a sort of whisper, often
pointing to my sick friend, who was at the further end of the hut; and
did not appear at all to wish for any reply. After remaining nearly half
an hour, and feeling and rubbing repeatedly my hands, face, and
head, which she uncovered by taking off my cap and turban, she
took her leave, apparently much gratified by her visit.
Drawn by Major Denham. Engraved by E. Finden.

THE RIVER SHARY, FROM THE WALLS OF KUSSERY.

Published by John Murray, London. Feb. 1826.

The river here is a wide, handsome stream, and the walls extend
quite to the banks, and have two water-gates; the character is the
same as nearer its embouchure. I passed one of these water-gates
at sunset, and was much struck by the beauty of the landscape, with
the fishing canoes just returning towards Loggun: the stream sweeps
off to the south-south-west, and then to the south. Loggun was said
to be thirty miles distant by the river. Here my poor friend declared it
impossible to remain, and we moved on towards Loggun the next
morning. We could advance, however, but a few miles. Mr. Toole’s
sufferings were most acute; he twice fainted, and we lifted him on
and off his horse like an infant, so helpless had he become. What
added also to our distress was, that from this time until the evening
of the 16th, the Shouaa Arabs, who occupy the frontier of the
Loggun country, refused to allow us to pass until the sultan had been
consulted, and a number of his questions answered as to the
purpose of our visit. We were now close to the river, and
notwithstanding the heat, the only means we had of defending either
ourselves or our animals from the torture of the millions of insects
that beset us, was by lighting fires at the entrance of our tent, and
constantly supplying them with weeds and wet straw: the thick
suffocating smoke arising from this description of fire afforded us
temporary relief. I rode down to the river, which here flows with great
beauty and majesty past the high walls of this capital of Loggun; it
comes direct from the south-west, with a rapid current. We entered
the town by the western gate, which leads to the principal street: it is
as wide as Pall Mall, and has large dwellings on each side, built with
great uniformity, each having a court-yard in front, surrounded by
walls, and a handsome entrance, with a strong door hasped with
iron: a number of the inhabitants were seated at their doors for the
purpose of seeing us enter, with their slaves ranged behind them. At
first they took but little notice of us: indeed, our appearance could not
have been very imposing: one of our party was laid on a camel, and
another supported on his horse by two persons, who walked on each
side of him, while he raved most incoherently from the violence of
the fever by which he was consuming. At length, however, a person
of apparent consequence advanced towards my horse, bending
nearly double, and joining his hands (the first salutation of the kind
that I had seen), followed by his slaves stooping still lower than
himself. After explaining that he was deputed by the sultan to
welcome kab n’jaffy (the white man), and repeating frequently that
he was kaffama (my friend), he preceded our party; and, as we
moved on, each assembly that we passed rose from the ground,
advanced towards us, and saluted us in the same manner as I have
already described. We were at length conducted to our habitation,
which consisted of four separate huts, well built, within an outer wall,
with a large entrance hall for our servants: in the most retired and
quiet spot I spread the mat and pillow of my patient, who was in a
sad state of exhaustion and irritation.
 The next morning I was sent for to appear before the sultan: ten
immense negroes, of high birth, most of them gray-bearded, bare-
headed, and carrying large clubs, preceded me through the streets,
and I was received with considerable ceremony. After passing
through several dark rooms, I was conducted to a large square court,
where some hundred persons were assembled, and all seated on
the ground: in the middle was a vacant space, to which they led me,
and I was desired to sit down also. Two slaves, in striped cotton
tobes, who were fanning the air through a lattice-work of cane,
pointed out the retirement of the sultan. On a signal, this shade was
removed, and something alive was discovered on a carpet, wrapped
up in silk tobes, with the head enveloped in shawls, and nothing but
the eyes visible: the whole court prostrated themselves, and poured
sand on their heads, while eight frumfrums and as many horns blew
a loud and very harsh-sounding salute.
My present, a red bornouse, a striped cotton caftan, a turban, two
knives, two pairs of scissors, and a pair of red trowsers, was laid
before him: he again whispered a welcome, for it is considered so
extremely ill-bred in a Loggun gentleman to speak out, that it is with
difficulty you can catch the sound of their voices.
He examined me very minutely, when the shade was again
drawn. I begged for permission to embark on the Shary, and was told
he would consider of it. He particularly inquired if I wished to
purchase b’lowy, or handsome female slaves, which I assured him I
did not; “because,” said he, “if you do, go no farther: I have some
hundreds, and will sell them to you as cheap as any one.”
Loggun, the capital of which country (Kernuk) is on the banks of
the Shary, and in 11° 7′ north latitude, is a very populous country.
Kernuk has fifteen thousand inhabitants at least. They speak a
language nearly Begharmi. The Shouaas are all round them, and to
them they are indebted for the plentiful supply of bullocks, milk, and
fat, with which the market abounds: these necessaries are paid for
by tobes, and blue cotton in stripes, which the Loggun people make
and dye of a very beautiful colour. They have, also, a metal currency
in Loggun, the first I had seen in Negroland: it consists of thin plates
of iron, something in the shape of the tip with which they shoe race-