This week's reading is Chapter 22.1 and 22.2 (Prokaryotes), Chapter 23.1 and 23.2 (Protists), 25.1 (Early Plant Life) and Chapter 27.1 and 27.2 (Animal Diversity) of the course textbook, which is acce
Biology
SENIOR CONTRIBUTING A UTHORS
C ONNIE R YE , EAST M ISSISSIPPI C OMMUNITY C OLLEGE
R OBERT W ISE , U NIVERSITY OF W ISCONSIN , O SHKOSH
V LADIMIR JURUKOVSKI , SUFFOLK C OUNTY C OMMUNITY C OLLEGE
JEAN D ESAIX , U NIVERSITY OF N ORTH C AROLINA AT C HAPEL H ILL
JUNG C HOI , G EORGIA INSTITUTE OF TECHNOLOGY
YAEL A VISSAR , R HODE ISLAND C OLLEGE
21 | VIRUSES
Figure 21.1 The tobacco mosaic virus (left), seen here by transmission electron microscopy, was the first virus to be
discovered. The virus causes disease in tobacco and other plants, such as the orchid (right). (credit a: USDA ARS;
credit b: modification of work by USDA Forest Service, Department of Plant Pathology Archive North Carolina State
University; scale-bar data from Matt Russell)
Chapter Outline
21.1: Viral Evolution, Morphology, and Classification
21.2: Virus Infections and Hosts
21.3: Prevention and Treatment of Viral Infections
21.4: Other Acellular Entities: Prions and Viroids
Introduction
No one knows exactly when viruses emerged or from where they came, since viruses do not leave historical footprints such
as fossils. Modern viruses are thought to be a mosaic of bits and pieces of nucleic acids picked up from various sources
along their respective evolutionary paths. Viruses are acellular, parasitic entities that are not classified within any kingdom.
Unlike most living organisms, viruses are not cells and cannot divide. Instead, they infect a host cell and use the host’s
replication processes to produce identical progeny virus particles. Viruses infect organisms as diverse as bacteria, plants,
and animals. They exist in a netherworld between a living organism and a nonliving entity. Living things grow, metabolize,
and reproduce. Viruses replicate, but to do so, they are entirely dependent on their host cells. They do not metabolize or
grow, but are assembled in their mature form.
21.1 | Viral Evolution, Morphology, and Classification
By the end of this section, you will be able to:
• Describe how viruses were first discovered and how they are detected
• Discuss three hypotheses about how viruses evolved
• Recognize the basic shapes of viruses
• Understand past and emerging classification systems for viruses
Viruses are diverse entities. They vary in their structure, their replication methods, and in their target hosts. Nearly all forms
of life—from bacteria and archaea to eukaryotes such as plants, animals, and fungi—have viruses that infect them. While
most biological diversity can be understood through evolutionary history, such as how species have adapted to conditions
and environments, much about virus origins and evolution remains unknown.
Chapter 21 | Viruses 535 Discovery and Detection
Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could
remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of
tobacco plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one via liquid plant extracts.
In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur
filter had removed all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable”
infectious agents were not simply very small bacteria but were a new type of very small, disease-causing particle.
Virions , single virus particles, are very small, about 20–250 nanometers in diameter. These individual virus particles are the
infectious form of a virus outside the host cell. Unlike bacteria (which are about 100-times larger), we cannot see viruses
with a light microscope, with the exception of some large virions of the poxvirus family. It was not until the development of
the electron microscope in the late 1930s that scientists got their first good view of the structure of the tobacco mosaic virus
(TMV) ( Figure 21.1 ) and other viruses ( Figure 21.2 ). The surface structure of virions can be observed by both scanning
and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a
transmission electron microscope. The use of these technologies has allowed for the discovery of many viruses of all types
of living organisms. They were initially grouped by shared morphology. Later, groups of viruses were classified by the type
of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More recently,
molecular analysis of viral replicative cycles has further refined their classification.
Figure 21.2 In these transmission electron micrographs, (a) a virus is dwarfed by the bacterial cell it infects, while (b)
these E. coli cells are dwarfed by cultured colon cells. (credit a: modification of work by U.S. Dept. of Energy, Office of
Science, LBL, PBD; credit b: modification of work by J.P. Nataro and S. Sears, unpub. data, CDC; scale-bar data from
Matt Russell)
Evolution of Viruses
Although biologists have accumulated a significant amount of knowledge about how present-day viruses evolve, much
less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms,
scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, so researchers must
conjecture by investigating how today’s viruses evolve and by using biochemical and genetic information to create
speculative virus histories.
While most findings agree that viruses don’t have a single common ancestor, scholars have yet to find a single hypothesis
about virus origins that is fully accepted in the field. One such hypothesis, called devolution or the regressive hypothesis,
proposes to explain the origin of viruses by suggesting that viruses evolved from free-living cells. However, many
components of how this process might have occurred are a mystery. A second hypothesis (called escapist or the progressive
hypothesis) accounts for viruses having either an RNA or a DNA genome and suggests that viruses originated from RNA
and DNA molecules that escaped from a host cell. A third hypothesis posits a system of self-replication similar to that of
536 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 other self-replicating molecules, likely evolving alongside the cells they rely on as hosts; studies of some plant pathogens
support this hypothesis.
As technology advances, scientists may develop and refine further hypotheses to explain the origin of viruses. The emerging
field called virus molecular systematics attempts to do just that through comparisons of sequenced genetic material. These
researchers hope to one day better understand the origin of viruses, a discovery that could lead to advances in the treatments
for the ailments they produce.
Viral Morphology
Viruses are acellular , meaning they are biological entities that do not have a cellular structure. They therefore lack most of
the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core,
an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived
from the host cell. Viruses may also contain additional proteins, such as enzymes. The most obvious difference between
members of viral families is their morphology, which is quite diverse. An interesting feature of viral complexity is that the
complexity of the host does not correlate with the complexity of the virion. Some of the most complex virion structures are
observed in bacteriophages, viruses that infect the simplest living organisms, bacteria.
Morphology
Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family. All virions have a nucleic
acid genome covered by a protective layer of proteins, called a capsid . The capsid is made up of protein subunits called
capsomeres . Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure.
In general, the shapes of viruses are classified into four groups: filamentous, isometric (or icosahedral), enveloped, and head
and tail. Filamentous viruses are long and cylindrical. Many plant viruses are filamentous, including TMV. Isometric viruses
have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding
capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is
similar to icosahedral viruses and a tail shape like filamentous viruses.
Many viruses use some sort of glycoprotein to attach to their host cells via molecules on the cell called viral receptors
(Figure 21.3 ). For these viruses, attachment is a requirement for later penetration of the cell membrane, so they can
complete their replication inside the cell. The receptors that viruses use are molecules that are normally found on cell
surfaces and have their own physiological functions. Viruses have simply evolved to make use of these molecules for their
own replication. For example, HIV uses the CD4 molecule on T lymphocytes as one of its receptors. CD4 is a type of
molecule called a cell adhesion molecule, which functions to keep different types of immune cells in close proximity to
each other during the generation of a T lymphocyte immune response.
Figure 21.3 The KSHV virus binds the xCT receptor on the surface of human cells. xCT receptors protect cells against
stress. Stressed cells express more xCT receptors than non-stressed cells. The KSHV virion causes cells to become
stressed, thereby increasing expression of the receptor to which it binds. (credit: modification of work by NIAID, NIH)
Chapter 21 | Viruses 537 Among the most complex virions known, the T4 bacteriophage, which infects the Escherichia coli bacterium, has a tail
structure that the virus uses to attach to host cells and a head structure that houses its DNA.
Adenovirus, a non-enveloped animal virus that causes respiratory illnesses in humans, uses glycoprotein spikes protruding
from its capsomeres to attach to host cells. Non-enveloped viruses also include those that cause polio (poliovirus), plantar
warts (papillomavirus), and hepatitis A (hepatitis A virus).
Enveloped virions like HIV, the causative agent in AIDS, consist of nucleic acid (RNA in the case of HIV) and capsid
proteins surrounded by a phospholipid bilayer envelope and its associated proteins. Glycoproteins embedded in the viral
envelope are used to attach to host cells. Other envelope proteins are the matrix proteins that stabilize the envelope and
often play a role in the assembly of progeny virions. Chicken pox, influenza, and mumps are examples of diseases caused
by viruses with envelopes. Because of the fragility of the envelope, non-enveloped viruses are more resistant to changes in
temperature, pH, and some disinfectants than enveloped viruses.
Overall, the shape of the virion and the presence or absence of an envelope tell us little about what disease the virus may
cause or what species it might infect, but they are still useful means to begin viral classification ( Figure 21.4 ).
Figure 21.4 Viruses can be either complex in shape or relatively simple. This figure shows three relatively
complex virions: the bacteriophage T4, with its DNA-containing head group and tail fibers that attach to host cells;
adenovirus, which uses spikes from its capsid to bind to host cells; and HIV, which uses glycoproteins embedded
in its envelope to bind to host cells. Notice that HIV has proteins called matrix proteins, internal to the envelope,
which help stabilize virion shape. (credit “bacteriophage, adenovirus”: modification of work by NCBI, NIH; credit
“HIV retrovirus”: modification of work by NIAID, NIH)
Which of the following statements about virus structure is true?
a. All viruses are encased in a viral membrane.
b. The capsomere is made up of small protein subunits called capsids.
c. DNA is the genetic material in all viruses.
d. Glycoproteins help the virus attach to the host cell.
Types of Nucleic Acid
Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA as theirs.
The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only
538 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 those genes that encode proteins that the virus cannot get from the host cell. This genetic material may be single- or double-
stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have
several, which are called segments.
In DNA viruses, the viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral genome and
to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases, such as chickenpox, hepatitis
B, and some venereal diseases, like herpes and genital warts.
RNA viruses contain only RNA as their genetic material. To replicate their genomes in the host cell, the RNA viruses
encode enzymes that can replicate RNA into DNA, which cannot be done by the host cell. These RNA polymerase enzymes
are more likely to make copying errors than DNA polymerases, and therefore often make mistakes during transcription. For
this reason, mutations in RNA viruses occur more frequently than in DNA viruses. This causes them to change and adapt
more rapidly to their host. Human diseases caused by RNA viruses include hepatitis C, measles, and rabies.
Virus Classification
To understand the features shared among different groups of viruses, a classification scheme is necessary. As most viruses
are not thought to have evolved from a common ancestor, however, the methods that scientists use to classify living things
are not very useful. Biologists have used several classification systems in the past, based on the morphology and genetics
of the different viruses. However, these earlier classification methods grouped viruses differently, based on which features
of the virus they were using to classify them. The most commonly used classification method today is called the Baltimore
classification scheme and is based on how messenger RNA (mRNA) is generated in each particular type of virus.
Past Systems of Classification
Viruses are classified in several ways: by factors such as their core content ( Table 21.1 and Figure 21.3 ), the structure
of their capsids, and whether they have an outer envelope. The type of genetic material (DNA or RNA) and its structure
(single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core
structures.
Virus Classification by Genome Structure and Core
Core Classifications Examples
RNA
DNA
Rabies virus, retroviruses
Herpesviruses, smallpox virus
Single-stranded
Double-stranded
Rabies virus, retroviruses
Herpesviruses, smallpox virus
Linear
Circular
Rabies virus, retroviruses, herpesviruses,
smallpox virus
Papillomaviruses, many bacteriophages
Non-segmented: genome consists of a single segment of
genetic material
Segmented: genome is divided into multiple segments
Parainfluenza viruses
Influenza viruses
Table 21.1
Chapter 21 | Viruses 539 Figure 21.5 Viruses are classified based on their core genetic material and capsid design. (a) Rabies virus has a
single-stranded RNA (ssRNA) core and an enveloped helical capsid, whereas (b) variola virus, the causative agent of
smallpox, has a double-stranded DNA (dsDNA) core and a complex capsid. Rabies transmission occurs when saliva
from an infected mammal enters a wound. The virus travels through neurons in the peripheral nervous system to the
central nervous system where it impairs brain function, and then travels to other tissues. The virus can infect any
mammal, and most die within weeks of infection. Smallpox is a human virus transmitted by inhalation of the variola
virus, localized in the skin, mouth, and throat, which causes a characteristic rash. Before its eradication in 1979,
infection resulted in a 30–35 percent mortality rate. (credit “rabies diagram”: modification of work by CDC; “rabies
micrograph”: modification of work by Dr. Fred Murphy, CDC; credit “small pox micrograph”: modification of work by Dr.
Fred Murphy, Sylvia Whitfield, CDC; credit “smallpox photo”: modification of work by CDC; scale-bar data from Matt
Russell)
Viruses can also be classified by the design of their capsids ( Figure 21.4 and Figure 21.5 ). Capsids are classified as naked
icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex ( Figure 21.6 and Figure 21.7 ). The type
of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-
segmented) are used to classify the virus core structures ( Table 21.2 ).
Figure 21.6 Adenovirus (left) is depicted with a double-stranded DNA genome enclosed in an icosahedral capsid that
is 90–100 nm across. The virus, shown clustered in the micrograph (right), is transmitted orally and causes a variety of
illnesses in vertebrates, including human eye and respiratory infections. (credit “adenovirus”: modification of work by
Dr. Richard Feldmann, National Cancer Institute; credit “micrograph”: modification of work by Dr. G. William Gary, Jr.,
CDC; scale-bar data from Matt Russell)
540 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Virus Classification by Capsid Structure
Capsid Classification Examples
Naked icosahedral Hepatitis A virus, polioviruses
Enveloped icosahedral Epstein-Barr virus, herpes simplex virus, rubella
virus, yellow fever virus, HIV-1
Enveloped helical Influenza viruses, mumps virus, measles virus,
rabies virus
Naked helical Tobacco mosaic virus
Complex with many proteins; some have combinations of
icosahedral and helical capsid structures
Herpesviruses, smallpox virus, hepatitis B virus,
T4 bacteriophage
Table 21.2
Figure 21.7 Transmission electron micrographs of various viruses show their structures. The capsid of the (a) polio
virus is naked icosahedral; (b) the Epstein-Barr virus capsid is enveloped icosahedral; (c) the mumps virus capsid is
an enveloped helix; (d) the tobacco mosaic virus capsid is naked helical; and (e) the herpesvirus capsid is complex.
(credit a: modification of work by Dr. Fred Murphy, Sylvia Whitfield; credit b: modification of work by Liza Gross; credit
c: modification of work by Dr. F. A. Murphy, CDC; credit d: modification of work by USDA ARS; credit e: modification of
work by Linda Stannard, Department of Medical Microbiology, University of Cape Town, South Africa, NASA; scale-bar
data from Matt Russell)
Baltimore Classification
The most commonly used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore
in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification
scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus.
Group I viruses contain double-stranded DNA (dsDNA) as their genome. Their mRNA is produced by transcription in
much the same way as with cellular DNA. Group II viruses have single-stranded DNA (ssDNA) as their genome. They
convert their single-stranded genomes into a dsDNA intermediate before transcription to mRNA can occur. Group III
viruses use dsRNA as their genome. The strands separate, and one of them is used as a template for the generation of mRNA
using the RNA-dependent RNA polymerase encoded by the virus. Group IV viruses have ssRNA as their genome with a
positive polarity. Positive polarity means that the genomic RNA can serve directly as mRNA. Intermediates of dsRNA,
called replicative intermediates , are made in the process of copying the genomic RNA. Multiple, full-length RNA strands
Chapter 21 | Viruses 541 of negative polarity (complimentary to the positive-stranded genomic RNA) are formed from these intermediates, which
may then serve as templates for the production of RNA with positive polarity, including both full-length genomic RNA
and shorter viral mRNAs. Group V viruses contain ssRNA genomes with a negative polarity , meaning that their sequence
is complementary to the mRNA. As with Group IV viruses, dsRNA intermediates are used to make copies of the genome
and produce mRNA. In this case, the negative-stranded genome can be converted directly to mRNA. Additionally, full-
length positive RNA strands are made to serve as templates for the production of the negative-stranded genome. Group
VI viruses have diploid (two copies) ssRNA genomes that must be converted, using the enzyme reverse transcriptase ,to
dsDNA; the dsDNA is then transported to the nucleus of the host cell and inserted into the host genome. Then, mRNA can
be produced by transcription of the viral DNA that was integrated into the host genome. Group VII viruses have partial
dsDNA genomes and make ssRNA intermediates that act as mRNA, but are also converted back into dsDNA genomes by
reverse transcriptase, necessary for genome replication. The characteristics of each group in the Baltimore classification are
summarized in Table 21.3 with examples of each group.
Baltimore Classification
Group Characteristics Mode of mRNA Production Example
I Double-stranded
DNA mRNA is transcribed directly from the DNA template Herpes simplex
(herpesvirus)
II Single-stranded
DNA
DNA is converted to double-stranded form before RNA is
transcribed
Canine
parvovirus
(parvovirus)
III Double-stranded
RNA mRNA is transcribed from the RNA genome
Childhood
gastroenteritis
(rotavirus)
IV Single stranded
RNA (+) Genome functions as mRNA Common cold
(pircornavirus)
V Single stranded
RNA (-) mRNA is transcribed from the RNA genome Rabies
(rhabdovirus)
VI
Single stranded
RNA viruses with
reverse
transcriptase
Reverse transcriptase makes DNA from the RNA
genome; DNA is then incorporated in the host genome;
mRNA is transcribed from the incorporated DNA
Human
immunodeficiency
virus (HIV)
VII
Double stranded
DNA viruses with
reverse
transcriptase
The viral genome is double-stranded DNA, but viral DNA
is replicated through an RNA intermediate; the RNA may
serve directly as mRNA or as a template to make mRNA
Hepatitis B virus
(hepadnavirus)
Table 21.3
21.2 | Virus Infections and Hosts
By the end of this section, you will be able to:
• List the steps of replication and explain what occurs at each step
• Describe the lytic and lysogenic cycles of virus replication
• Explain the transmission and diseases of animal and plant viruses
• Discuss the economic impact of animal and plant viruses
Viruses can be seen as obligate, intracellular parasites. A virus must attach to a living cell, be taken inside, manufacture its
proteins and copy its genome, and find a way to escape the cell so that the virus can infect other cells. Viruses can infect only
542 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 certain species of hosts and only certain cells within that host. Cells that a virus may use to replicate are called permissive .
For most viruses, the molecular basis for this specificity is that a particular surface molecule known as the viral receptor
must be found on the host cell surface for the virus to attach. Also, metabolic and host cell immune response differences
seen in different cell types based on differential gene expression are a likely factor in which cells a virus may target for
replication. The permissive cell must make the substances that the virus needs or the virus will not be able to replicate there.
Steps of Virus Infections
A virus must use cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural
changes in the host cell, which may cause cell damage. These changes, called cytopathic (causing cell damage) effects,
can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus
known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all
progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to
control and eliminate the virus from the body, and from cell damage caused by the virus. Many animal viruses, such as
HIV (human immunodeficiency virus), leave the infected cells of the immune system by a process known as budding ,
where virions leave the cell individually. During the budding process, the cell does not undergo lysis and is not immediately
killed. However, the damage to the cells that the virus infects may make it impossible for the cells to function normally,
even though the cells remain alive for a period of time. Most productive viral infections follow similar steps in the virus
replication cycle: attachment, penetration, uncoating, replication, assembly, and release ( Figure 21.8 ).
Attachment
A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via
glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host—and the cells within
the host—that can be infected by a particular virus. This can be illustrated by thinking of several keys and several locks,
where each key will fit only one specific lock.
This video (http://openstaxcollege.org/l/influenza) explains how influenza attacks the body.
Entry
The nucleic acid of bacteriophages enters the host cell naked, leaving the capsid outside the cell. Plant and animal viruses
can enter through endocytosis, in which the cell membrane surrounds and engulfs the entire virus. Some enveloped viruses
enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell, the viral capsid is
degraded, and the viral nucleic acid is released, which then becomes available for replication and transcription.
Replication and Assembly
The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to
make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis.
RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA
directs the host cell to synthesize viral enzymes and capsid proteins, and assemble new virions. Of course, there are
exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes supply
the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must
be reverse transcribed into DNA, which then is incorporated into the host cell genome. They are within group VI of the
Baltimore classification scheme. To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific
enzyme reverse transcriptase that transcribes an RNA template to DNA. Reverse transcription never occurs in uninfected
host cells—the needed enzyme reverse transcriptase is only derived from the expression of viral genes within the infected
host cells. The fact that HIV produces some of its own enzymes not found in the host has allowed researchers to develop
drugs that inhibit these enzymes. These drugs, including the reverse transcriptase inhibitor AZT , inhibit HIV replication by
reducing the activity of the enzyme without affecting the host’s metabolism. This approach has led to the development of a
variety of drugs used to treat HIV and has been effective at reducing the number of infectious virions (copies of viral RNA)
in the blood to non-detectable levels in many HIV-infected individuals.
Chapter 21 | Viruses 543 Egress
The last stage of viral replication is the release of the new virions produced in the host organism, where they are able to
infect adjacent cells and repeat the replication cycle. As you’ve learned, some viruses are released when the host cell dies,
and other viruses can leave infected cells by budding through the membrane without directly killing the cell.
Figure 21.8 In influenza virus infection, glycoproteins attach to a host epithelial cell. As a result, the virus is
engulfed. RNA and proteins are made and assembled into new virions.
Influenza virus is packaged in a viral envelope that fuses with the plasma membrane. This way, the virus
can exit the host cell without killing it. What advantage does the virus gain by keeping the host cell alive?
Wa t c h a video (https://www.khanacademy.org/science/biology/her/tree-of-life/v/viruses) on viruses, identifying
structures, modes of transmission, replication, and more.
Different Hosts and Their Viruses
As you’ve learned, viruses are often very specific as to which hosts and which cells within the host they will infect. This
feature of a virus makes it specific to one or a few species of life on Earth. On the other hand, so many different types
of viruses exist on Earth that nearly every living organism has its own set of viruses that tries to infect its cells. Even the
smallest and simplest of cells, prokaryotic bacteria, may be attacked by specific types of viruses.
544 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Bacteriophages
Figure 21.9 This transmission electron micrograph shows bacteriophages attached to a bacterial cell. (credit:
modification of work by Dr. Graham Beards; scale-bar data from Matt Russell)
Bacteriophages are viruses that infect bacteria ( Figure 21.9 ). When infection of a cell by a bacteriophage results in the
production of new virions, the infection is said to be productive . If the virions are released by bursting the cell, the virus
replicates by means of a lytic cycle (Figure 21.10 ). An example of a lytic bacteriophage is T4, which infects Escherichia
coli found in the human intestinal tract. Sometimes, however, a virus can remain within the cell without being released. For
example, when a temperate bacteriophage infects a bacterial cell, it replicates by means of a lysogenic cycle (Figure 21.10 ),
and the viral genome is incorporated into the genome of the host cell. When the phage DNA is incorporated into the host
cell genome, it is called a prophage . An example of a lysogenic bacteriophage is the λ (lambda) virus, which also infects
the E.coli bacterium. Viruses that infect plant or animal cells may also undergo infections where they are not producing
virions for long periods. An example is the animal herpesviruses, including herpes simplex viruses, the cause of oral and
genital herpes in humans. In a process called latency , these viruses can exist in nervous tissue for long periods of time
without producing new virions, only to leave latency periodically and cause lesions in the skin where the virus replicates.
Even though there are similarities between lysogeny and latency, the term lysogenic cycle is usually reserved to describe
bacteriophages. Latency will be described in more detail below.
Chapter 21 | Viruses 545 Figure 21.10 A temperate bacteriophage has both lytic and lysogenic cycles. In the lytic cycle, the phage
replicates and lyses the host cell. In the lysogenic cycle, phage DNA is incorporated into the host genome,
where it is passed on to subsequent generations. Environmental stressors such as starvation or exposure to toxic
chemicals may cause the prophage to excise and enter the lytic cycle.
Which of the following statements is false?
a. In the lytic cycle, new phage are produced and released into the environment.
b. In the lysogenic cycle, phage DNA is incorporated into the host genome.
c. An environmental stressor can cause the phage to initiate the lysogenic cycle.
d. Cell lysis only occurs in the lytic cycle.
Animal Viruses
Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell.
Non-enveloped or “naked” animal viruses may enter cells in two different ways. As a protein in the viral capsid binds to
its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of receptor-
mediated endocytosis. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to
undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then
“injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages. Enveloped
viruses also have two ways of entering cells after binding to their receptors: receptor-mediated endocytosis, or fusion . Many
enveloped viruses enter the cell by receptor-mediated endocytosis in a fashion similar to some non-enveloped viruses. On
the other hand, fusion only occurs with enveloped virions. These viruses, which include HIV among others, use special
fusion proteins in their envelopes to cause the envelope to fuse with the plasma membrane of the cell, thus releasing the
genome and capsid of the virus into the cell cytoplasm.
After making their proteins and copying their genomes, animal viruses complete the assembly of new virions and exit the
cell. As we have already discussed using the example of HIV, enveloped animal viruses may bud from the cell membrane as
they assemble themselves, taking a piece of the cell’s plasma membrane in the process. On the other hand, non-enveloped
viral progeny, such as rhinoviruses, accumulate in infected cells until there is a signal for lysis or apoptosis, and all virions
are released together.
546 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 As you will learn in the next module, animal viruses are associated with a variety of human diseases. Some of them follow
the classic pattern of acute disease , where symptoms get increasingly worse for a short period followed by the elimination
of the virus from the body by the immune system and eventual recovery from the infection. Examples of acute viral
diseases are the common cold and influenza. Other viruses cause long-term chronic infections , such as the virus causing
hepatitis C, whereas others, like herpes simplex virus, only cause intermittent symptoms. Still other viruses, such as
human herpesviruses 6 and 7, which in some cases can cause the minor childhood disease roseola, often successfully cause
productive infections without causing any symptoms at all in the host, and thus we say these patients have an asymptomatic
infection .
In hepatitis C infections, the virus grows and reproduces in liver cells, causing low levels of liver damage. The damage is
so low that infected individuals are often unaware that they are infected, and many infections are detected only by routine
blood work on patients with risk factors such as intravenous drug use. On the other hand, since many of the symptoms
of viral diseases are caused by immune responses, a lack of symptoms is an indication of a weak immune response to the
virus. This allows for the virus to escape elimination by the immune system and persist in individuals for years, all the while
producing low levels of progeny virions in what is known as a chronic viral disease. Chronic infection of the liver by this
virus leads to a much greater chance of developing liver cancer, sometimes as much as 30 years after the initial infection.
As already discussed, herpes simplex virus can remain in a state of latency in nervous tissue for months, even years. As
the virus “hides” in the tissue and makes few if any viral proteins, there is nothing for the immune response to act against,
and immunity to the virus slowly declines. Under certain conditions, including various types of physical and psychological
stress, the latent herpes simplex virus may be reactivated and undergo a lytic replication cycle in the skin, causing the lesions
associated with the disease. Once virions are produced in the skin and viral proteins are synthesized, the immune response
is again stimulated and resolves the skin lesions in a few days by destroying viruses in the skin. As a result of this type of
replicative cycle, appearances of cold sores and genital herpes outbreaks only occur intermittently, even though the viruses
remain in the nervous tissue for life. Latent infections are common with other herpesviruses as well, including the varicella-
zoster virus that causes chickenpox. After having a chickenpox infection in childhood, the varicella-zoster virus can remain
latent for many years and reactivate in adults to cause the painful condition known as “shingles” ( Figure 21.11 ab ).
Figure 21.11 (a) Varicella-zoster, the virus that causes chickenpox, has an enveloped icosahedral capsid visible in this
transmission electron micrograph. Its double-stranded DNA genome becomes incorporated in the host DNA and can
reactivate after latency in the form of (b) shingles, often exhibiting a rash. (credit a: modification of work by Dr. Erskine
Palmer, B. G. Martin, CDC; credit b: modification of work by “rosmary”/Flickr; scale-bar data from Matt Russell)
Some animal-infecting viruses, including the hepatitis C virus discussed above, are known as oncogenic viruses : They
have the ability to cause cancer. These viruses interfere with the normal regulation of the host cell cycle either by either
introducing genes that stimulate unregulated cell growth (oncogenes) or by interfering with the expression of genes that
inhibit cell growth. Oncogenic viruses can be either DNA or RNA viruses. Cancers known to be associated with viral
infections include cervical cancer caused by human papillomavirus (HPV) ( Figure 21.12 ), liver cancer caused by hepatitis
B virus, T-cell leukemia, and several types of lymphoma.
Chapter 21 | Viruses 547 Figure 21.12 HPV, or human papillomavirus, has a naked icosahedral capsid visible in this transmission electron
micrograph and a double-stranded DNA genome that is incorporated into the host DNA. The virus, which is sexually
transmitted, is oncogenic and can lead to cervical cancer. (credit: modification of work by NCI, NIH; scale-bar data from
Matt Russell)
Visit the interactive animations (http://openstaxcollege.org/l/animal_viruses) showing the various stages of the
replicative cycles of animal viruses and click on the flash animation links.
Plant Viruses
Plant viruses, like other viruses, contain a core of either DNA or RNA. You have already learned about one of these, the
tobacco mosaic virus. As plant viruses have a cell wall to protect their cells, these viruses do not use receptor-mediated
endocytosis to enter host cells as is seen with animal viruses. For many plant viruses to be transferred from plant to plant,
damage to some of the plants’ cells must occur to allow the virus to enter a new host. This damage is often caused by
weather, insects, animals, fire, or human activities like farming or landscaping. Additionally, plant offspring may inherit
viral diseases from parent plants. Plant viruses can be transmitted by a variety of vectors, through contact with an infected
plant’s sap, by living organisms such as insects and nematodes, and through pollen. When plants viruses are transferred
between different plants, this is known as horizontal transmission , and when they are inherited from a parent, this is called
vertical transmission .
Symptoms of viral diseases vary according to the virus and its host ( Table 21.4 ). One common symptom is hyperplasia , the
abnormal proliferation of cells that causes the appearance of plant tumors known as galls . Other viruses induce hypoplasia ,
or decreased cell growth, in the leaves of plants, causing thin, yellow areas to appear. Still other viruses affect the plant by
directly killing plant cells, a process known as cell necrosis . Other symptoms of plant viruses include malformed leaves,
black streaks on the stems of the plants, altered growth of stems, leaves, or fruits, and ring spots, which are circular or linear
areas of discoloration found in a leaf.
548 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Some Common Symptoms of Plant Viral Diseases
Symptom Appears as
Hyperplasia Galls (tumors)
Hypoplasia Thinned, yellow splotches on leaves
Cell necrosis Dead, blackened stems, leaves, or fruit
Abnormal growth patterns Malformed stems, leaves, or fruit
Discoloration Yellow, red, or black lines, or rings in stems, leaves, or fruit
Table 21.4
Plant viruses can seriously disrupt crop growth and development, significantly affecting our food supply. They are
responsible for poor crop quality and quantity globally, and can bring about huge economic losses annually. Others viruses
may damage plants used in landscaping. Some viruses that infect agricultural food plants include the name of the plant
they infect, such as tomato spotted wilt virus, bean common mosaic virus, and cucumber mosaic virus. In plants used for
landscaping, two of the most common viruses are peony ring spot and rose mosaic virus. There are far too many plant
viruses to discuss each in detail, but symptoms of bean common mosaic virus result in lowered bean production and stunted,
unproductive plants. In the ornamental rose, the rose mosaic disease causes wavy yellow lines and colored splotches on the
leaves of the plant.
21.3 | Prevention and Treatment of Viral Infections
By the end of this section, you will be able to:
• Identify major viral illnesses that affect humans
• Compare vaccinations and anti-viral drugs as medical approaches to viruses
Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses
like meningitis ( Figure 21.13 ). These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as
HIV, are capable of both avoiding the immune response and mutating to become resistant to antiviral drugs.
Chapter 21 | Viruses 549 Figure 21.13 Viruses can cause dozens of ailments in humans, ranging from mild illnesses to serious diseases. (credit:
modification of work by Mikael Häggström)
Vaccines for Prevention
While we do have limited numbers of effective antiviral drugs, such as those used to treat HIV and influenza, the primary
method of controlling viral disease is by vaccination, which is intended to prevent outbreaks by building immunity to a
virus or virus family ( Figure 21.14 ).Vaccines may be prepared using live viruses, killed viruses, or molecular subunits of
the virus. The killed viral vaccines and subunit viruses are both incapable of causing disease.
Live viral vaccines are designed in the laboratory to cause few symptoms in recipients while giving them protective
immunity against future infections. Polio was one disease that represented a milestone in the use of vaccines. Mass
immunization campaigns in the 1950s (killed vaccine) and 1960s (live vaccine) significantly reduced the incidence of the
disease, which caused muscle paralysis in children and generated a great amount of fear in the general population when
regional epidemics occurred. The success of the polio vaccine paved the way for the routine dispensation of childhood
vaccines against measles, mumps, rubella, chickenpox, and other diseases.
The danger of using live vaccines, which are usually more effective than killed vaccines, is the low but significant
danger that these viruses will revert to their disease-causing form by back mutations . Live vaccines are usually made
by attenuating (weakening) the “wild-type” (disease-causing) virus by growing it in the laboratory in tissues or at
temperatures different from what the virus is accustomed to in the host. Adaptations to these new cells or temperatures
induce mutations in the genomes of the virus, allowing it to grow better in the laboratory while inhibiting its ability to cause
disease when reintroduced into conditions found in the host. These attenuated viruses thus still cause infection, but they do
not grow very well, allowing the immune response to develop in time to prevent major disease. Back mutations occur when
the vaccine undergoes mutations in the host such that it readapts to the host and can again cause disease, which can then be
spread to other humans in an epidemic. This type of scenario happened as recently as 2007 in Nigeria where mutations in a
polio vaccine led to an epidemic of polio in that country.
Some vaccines are in continuous development because certain viruses, such as influenza and HIV, have a high mutation rate
compared to other viruses and normal host cells. With influenza, mutations in the surface molecules of the virus help the
organism evade the protective immunity that may have been obtained in a previous influenza season, making it necessary
for individuals to get vaccinated every year. Other viruses, such as those that cause the childhood diseases measles, mumps,
and rubella, mutate so infrequently that the same vaccine is used year after year.
550 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 21.14 Vaccinations are designed to boost immunity to a virus to prevent infection. (credit: USACE Europe
District)
Watch this NOVA video (http://openstaxcollege.org/l/1918_flu) to learn how microbiologists are attempting to replicate
the deadly 1918 Spanish influenza virus so they can understand more about virology.
Vaccines and Anti-viral Drugs for Treatment
In some cases, vaccines can be used to treat an active viral infection. The concept behind this is that by giving the
vaccine, immunity is boosted without adding more disease-causing virus. In the case of rabies, a fatal neurological disease
transmitted via the saliva of rabies virus-infected animals, the progression of the disease from the time of the animal bite
to the time it enters the central nervous system may be 2 weeks or longer. This is enough time to vaccinate an individual
who suspects that they have been bitten by a rabid animal, and their boosted immune response is sufficient to prevent the
virus from entering nervous tissue. Thus, the potentially fatal neurological consequences of the disease are averted, and the
individual only has to recover from the infected bite. This approach is also being used for the treatment of Ebola, one of the
fastest and most deadly viruses on earth. Transmitted by bats and great apes, this disease can cause death in 70–90 percent
of infected humans within 2 weeks. Using newly developed vaccines that boost the immune response in this way, there is
hope that affected individuals will be better able to control the virus, potentially saving a greater percentage of infected
persons from a rapid and very painful death.
Another way of treating viral infections is the use of antiviral drugs. These drugs often have limited success in curing viral
disease, but in many cases, they have been used to control and reduce symptoms for a wide variety of viral diseases. For
most viruses, these drugs can inhibit the virus by blocking the actions of one or more of its proteins. It is important that the
targeted proteins be encoded by viral genes and that these molecules are not present in a healthy host cell. In this way, viral
growth is inhibited without damaging the host. There are large numbers of antiviral drugs available to treat infections, some
specific for a particular virus and others that can affect multiple viruses.
Antivirals have been developed to treat genital herpes (herpes simplex II) and influenza. For genital herpes, drugs such as
acyclovir can reduce the number and duration of episodes of active viral disease, during which patients develop viral lesions
in their skin cells. As the virus remains latent in nervous tissue of the body for life, this drug is not curative but can make the
symptoms of the disease more manageable. For influenza, drugs like Tamiflu (oseltamivir) ( Figure 21.15 ) can reduce the
duration of “flu” symptoms by 1 or 2 days, but the drug does not prevent symptoms entirely. Tamiflu works by inhibiting
Chapter 21 | Viruses 551 an enzyme (viral neuraminidase) that allows new virions to leave their infected cells. Thus, Tamiflu inhibits the spread of
virus from infected to uninfected cells. Other antiviral drugs, such as Ribavirin, have been used to treat a variety of viral
infections, although its mechanism of action against certain viruses remains unclear.
Figure 21.15 (a) Tamiflu inhibits a viral enzyme called neuraminidase (NA) found in the influenza viral envelope.
(b) Neuraminidase cleaves the connection between viral hemagglutinin (HA), also found in the viral envelope, and
glycoproteins on the host cell surface. Inhibition of neuraminidase prevents the virus from detaching from the host cell,
thereby blocking further infection. (credit a: modification of work by M. Eickmann)
By far, the most successful use of antivirals has been in the treatment of the retrovirus HIV, which causes a disease that, if
untreated, is usually fatal within 10–12 years after infection. Anti-HIV drugs have been able to control viral replication to
the point that individuals receiving these drugs survive for a significantly longer time than the untreated.
Anti-HIV drugs inhibit viral replication at many different phases of the HIV replicative cycle ( Figure 21.16 ). Drugs
have been developed that inhibit the fusion of the HIV viral envelope with the plasma membrane of the host cell (fusion
inhibitors), the conversion of its RNA genome into double-stranded DNA (reverse transcriptase inhibitors), the integration
of the viral DNA into the host genome (integrase inhibitors), and the processing of viral proteins (protease inhibitors).
552 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 21.16 HIV, an enveloped, icosahedral virus, attaches to the CD4 receptor of an immune cell and fuses with
the cell membrane. Viral contents are released into the cell, where viral enzymes convert the single-stranded RNA
genome into DNA and incorporate it into the host genome. (credit: NIAID, NIH)
When any of these drugs are used individually, the high mutation rate of the virus allows it to easily and rapidly develop
resistance to the drug, limiting the drug’s effectiveness. The breakthrough in the treatment of HIV was the development
of HAART, highly active anti-retroviral therapy, which involves a mixture of different drugs, sometimes called a drug
“cocktail.” By attacking the virus at different stages of its replicative cycle, it is much more difficult for the virus to develop
resistance to multiple drugs at the same time. Still, even with the use of combination HAART therapy, there is concern that,
over time, the virus will develop resistance to this therapy. Thus, new anti-HIV drugs are constantly being developed with
the hope of continuing the battle against this highly fatal virus.
Chapter 21 | Viruses 553 Applied Virology
The study of viruses has led to the development of a variety of new ways to treat non-viral diseases.
Viruses have been used in gene therapy . Gene therapy is used to treat genetic diseases such as severe
combined immunodeficiency (SCID), a heritable, recessive disease in which children are born with severely
compromised immune systems. One common type of SCID is due to the lack of an enzyme, adenosine
deaminase (ADA), which breaks down purine bases. To treat this disease by gene therapy, bone marrow
cells are taken from a SCID patient and the ADA gene is inserted. This is where viruses come in, and
their use relies on their ability to penetrate living cells and bring genes in with them. Viruses such as
adenovirus, an upper respiratory human virus, are modified by the addition of the ADA gene, and the virus
then transports this gene into the cell. The modified cells, now capable of making ADA, are then given
back to the patients in the hope of curing them. Gene therapy using viruses as carrier of genes (viral
vectors), although still experimental, holds promise for the treatment of many genetic diseases. Still, many
technological problems need to be solved for this approach to be a viable method for treating genetic
disease.
Another medical use for viruses relies on their specificity and ability to kill the cells they infect. Oncolytic
viruses are engineered in the laboratory specifically to attack and kill cancer cells. A genetically modified
adenovirus known as H101 has been used since 2005 in clinical trials in China to treat head and neck
cancers. The results have been promising, with a greater short-term response rate to the combination of
chemotherapy and viral therapy than to chemotherapy treatment alone. This ongoing research may herald
the beginning of a new age of cancer therapy, where viruses are engineered to find and specifically kill
cancer cells, regardless of where in the body they may have spread.
A third use of viruses in medicine relies on their specificity and involves using bacteriophages in the
treatment of bacterial infections. Bacterial diseases have been treated with antibiotics since the 1940s.
However, over time, many bacteria have developed resistance to antibiotics. A good example is methicillin-
resistant Staphylococcus aureus (MRSA, pronounced “mersa”), an infection commonly acquired in
hospitals. This bacterium is resistant to a variety of antibiotics, making it difficult to treat. The use of
bacteriophages specific for such bacteria would bypass their resistance to antibiotics and specifically kill
them. Although phage therapy is in use in the Republic of Georgia to treat antibiotic-resistant bacteria,
its use to treat human diseases has not been approved in most countries. However, the safety of the
treatment was confirmed in the United States when the U.S. Food and Drug Administration approved
spraying meats with bacteriophages to destroy the food pathogen Listeria. As more and more antibiotic-
resistant strains of bacteria evolve, the use of bacteriophages might be a potential solution to the problem,
and the development of phage therapy is of much interest to researchers worldwide.
21.4 | Other Acellular Entities: Prions and Viroids
By the end of this section, you will be able to:
• Describe prions and their basic properties
• Define viroids and their targets of infection
Prions and viroids are pathogens (agents with the ability to cause disease) that have simpler structures than viruses but, in
the case of prions, still can produce deadly diseases.
Prions
Prions , so-called because they are proteinaceous, are infectious particles—smaller than viruses—that contain no nucleic
acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered
impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists
that such agents do indeed exist.
554 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle
(commonly known as “mad cow disease”) were shown to be transmitted by prions. The disease was spread by the
consumption of meat, nervous tissue, or internal organs between members of the same species. Kuru, native to humans in
Papua New Guinea, was spread from human to human via ritualistic cannibalism. BSE, originally detected in the United
Kingdom, was spread between cattle by the practice of including cattle nervous tissue in feed for other cattle. Individuals
with kuru and BSE show symptoms of loss of motor control and unusual behaviors, such as uncontrolled bursts of laughter
with kuru, followed by death. Kuru was controlled by inducing the population to abandon its ritualistic cannibalism.
On the other hand, BSE was initially thought to only affect cattle. Cattle dying of the disease were shown to have developed
lesions or “holes” in the brain, causing the brain tissue to resemble a sponge. Later on in the outbreak, however, it was
shown that a similar encephalopathy in humans known as variant Creutzfeldt-Jakob disease (CJD) could be acquired from
eating beef from animals with BSE, sparking bans by various countries on the importation of British beef and causing
considerable economic damage to the British beef industry ( Figure 21.17 ). BSE still exists in various areas, and although a
rare disease, individuals that acquire CJD are difficult to treat. The disease can be spread from human to human by blood,
so many countries have banned blood donation from regions associated with BSE.
The cause of spongiform encephalopathies, such as kuru and BSE, is an infectious structural variant of a normal cellular
protein called PrP (prion protein). It is this variant that constitutes the prion particle. PrP exists in two forms, PrP c, the
normal form of the protein, and PrP sc, the infectious form. Once introduced into the body, the PrP sccontained within the
prion binds to PrP cand converts it to PrP sc. This leads to an exponential increase of the PrP scprotein, which aggregates.
PrP scis folded abnormally, and the resulting conformation (shape) is directly responsible for the lesions seen in the brains
of infected cattle. Thus, although not without some detractors among scientists, the prion seems likely to be an entirely new
form of infectious agent, the first one found whose transmission is not reliant upon genes made of DNA or RNA.
Figure 21.17 (a) Endogenous normal prion protein (PrP c) is converted into the disease-causing form (PrP sc) when it
encounters this variant form of the protein. PrP sc may arise spontaneously in brain tissue, especially if a mutant form
of the protein is present, or it may occur via the spread of misfolded prions consumed in food into brain tissue. (b) This
prion-infected brain tissue, visualized using light microscopy, shows the vacuoles that give it a spongy texture, typical
of transmissible spongiform encephalopathies. (credit b: modification of work by Dr. Al Jenny, USDA APHIS; scale-bar
data from Matt Russell)
Viroids
Viroids are plant pathogens: small, single-stranded, circular RNA particles that are much simpler than a virus. They do not
have a capsid or outer envelope, but like viruses can reproduce only within a host cell. Viroids do not, however, manufacture
any proteins, and they only produce a single, specific RNA molecule. Human diseases caused by viroids have yet to be
identified.
Viroids are known to infect plants ( Figure 21.18 ) and are responsible for crop failures and the loss of millions of dollars
in agricultural revenue each year. Some of the plants they infect include potatoes, cucumbers, tomatoes, chrysanthemums,
avocados, and coconut palms.
Chapter 21 | Viruses 555 Figure 21.18 These potatoes have been infected by the potato spindle tuber viroid (PSTV), which is typically spread
when infected knives are used to cut healthy potatoes, which are then planted. (credit: Pamela Roberts, University of
Florida Institute of Food and Agricultural Sciences, USDA ARS)
556 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Virologist
Virology is the study of viruses, and a virologist is an individual trained in this discipline. Training in virology
can lead to many different career paths. Virologists are actively involved in academic research and teaching
in colleges and medical schools. Some virologists treat patients or are involved in the generation and
production of vaccines. They might participate in epidemiologic studies ( Figure 21.19 ) or become science
writers, to name just a few possible careers.
Figure 21.19 This virologist is engaged in fieldwork, sampling eggs from this nest for avian influenza. (credit: Don
Becker, USGS EROS, U.S. Fish and Wildlife Service)
If you think you may be interested in a career in virology, find a mentor in the field. Many large medical
centers have departments of virology, and smaller hospitals usually have virology labs within their
microbiology departments. Volunteer in a virology lab for a semester or work in one over the summer.
Discussing the profession and getting a first-hand look at the work will help you decide whether a career in
virology is right for you. The American Society of Virology’s website (http://openstaxcollege.org/l/asv) is
a good resource for information regarding training and careers in virology.
Chapter 21 | Viruses 557 acellular
acute disease
asymptomatic disease
attenuation
AZT
back mutation
bacteriophage
budding
capsid
capsomere
cell necrosis
chronic infection
cytopathic
envelope
fusion
gall
gene therapy
group I virus
group II virus
group III virus
group IV virus
group V virus
group VI virus
group VII virus
horizontal transmission
hyperplasia
hypoplasia
intermittent symptom
latency
lysis
KEY TERMS
lacking cells
disease where the symptoms rise and fall within a short period of time
disease where there are no symptoms and the individual is unaware of being infected unless lab
tests are performed
weakening of a virus during vaccine development
anti-HIV drug that inhibits the viral enzyme reverse transcriptase
when a live virus vaccine reverts back to it disease-causing phenotype
virus that infects bacteria
method of exit from the cell used in certain animal viruses, where virions leave the cell individually by capturing
a piece of the host plasma membrane
protein coating of the viral core
protein subunit that makes up the capsid
cell death
describes when the virus persists in the body for a long period of time
causing cell damage
lipid bilayer that envelopes some viruses
method of entry by some enveloped viruses, where the viral envelope fuses with the plasma membrane of the host
cell
appearance of a plant tumor
treatment of genetic disease by adding genes, using viruses to carry the new genes inside the cell
virus with a dsDNA genome
virus with a ssDNA genome
virus with a dsRNA genome
virus with a ssRNA genome with positive polarity
virus with a ssRNA genome with negative polarity
virus with a ssRNA genomes converted into dsDNA by reverse transcriptase
virus with a single-stranded mRNA converted into dsDNA for genome replication
transmission of a disease from parent to offspring
abnormally high cell growth and division
abnormally low cell growth and division
symptom that occurs periodically
virus that remains in the body for a long period of time but only causes intermittent symptoms
bursting of a cell
558 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 lysogenic cycle
lytic cycle
matrix protein
negative polarity
oncogenic virus
oncolytic virus
pathogen
permissive
phage therapy
positive polarity
prion
productive
prophage
PrP c
PrP sc
replicative intermediate
reverse transcriptase
vaccine
vertical transmission
viral receptor
virion
viroid
virus core
type of virus replication in which the viral genome is incorporated into the genome of the host cell
type of virus replication in which virions are released through lysis, or bursting, of the cell
envelope protein that stabilizes the envelope and often plays a role in the assembly of progeny virions
ssRNA viruses with genomes complimentary to their mRNA
virus that has the ability to cause cancer
virus engineered to specifically infect and kill cancer cells
agent with the ability to cause disease
cell type that is able to support productive replication of a virus
treatment of bacterial diseases using bacteriophages specific to a particular bacterium
ssRNA virus with a genome that contains the same base sequences and codons found in their mRNA
infectious particle that consists of proteins that replicate without DNA or RNA
viral infection that leads to the production of new virions
phage DNA that is incorporated into the host cell genome
normal prion protein
infectious form of a prion protein
dsRNA intermediate made in the process of copying genomic RNA
enzyme found in Baltimore groups VI and VII that converts single-stranded RNA into double-
stranded DNA
weakened solution of virus components, viruses, or other agents that produce an immune response
transmission of disease between unrelated individuals
glycoprotein used to attach a virus to host cells via molecules on the cell
individual virus particle outside a host cell
plant pathogen that produces only a single, specific RNA
contains the virus genome
CHAPTER SUMMARY
21.1 Viral Evolution, Morphology, and Classification
Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either
DNA or RNA—never both—and they replicate using the replication proteins of a host cell. Viruses are diverse, infecting
archaea, bacteria, fungi, plants, and animals. Viruses consist of a nucleic acid core surrounded by a protein capsid with or
without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements
of the classification of viruses. The most commonly used classification method, the Baltimore classification, categorizes
viruses based on how they produce their mRNA.
21.2 Virus Infections and Hosts
Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes
slowly killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration,
uncoating, replication, assembly, and release. A viral infection may be productive, resulting in new virions, or
Chapter 21 | Viruses 559 nonproductive, which means that the virus remains inside the cell without producing new virions. Bacteriophages are
viruses that infect bacteria. They have two different modes of replication: the lytic cycle, where the virus replicates and
bursts out of the bacteria, and the lysogenic cycle, which involves the incorporation of the viral genome into the bacterial
host genome. Animal viruses cause a variety of infections, with some causing chronic symptoms (hepatitis C), some
intermittent symptoms (latent viruses such a herpes simplex virus 1), and others that cause very few symptoms, if any
(human herpesviruses 6 and 7). Oncogenic viruses in animals have the ability to cause cancer by interfering with the
regulation of the host cell cycle. Viruses of plants are responsible for significant economic damage in both agriculture and
plants used for ornamentation.
21.3 Prevention and Treatment of Viral Infections
Viruses cause a variety of diseases in humans. Many of these diseases can be prevented by the use of viral vaccines, which
stimulate protective immunity against the virus without causing major disease. Viral vaccines may also be used in active
viral infections, boosting the ability of the immune system to control or destroy the virus. A series of antiviral drugs that
target enzymes and other protein products of viral genes have been developed and used with mixed success. Combinations
of anti-HIV drugs have been used to effectively control the virus, extending the lifespans of infected individuals. Viruses
have many uses in medicines, such as in the treatment of genetic disorders, cancer, and bacterial infections.
21.4 Other Acellular Entities: Prions and Viroids
Prions are infectious agents that consist of protein, but no DNA or RNA, and seem to produce their deadly effects by
duplicating their shapes and accumulating in tissues. They are thought to contribute to several progressive brain disorders,
including mad cow disease and Creutzfeldt-Jakob disease. Viroids are single-stranded RNA pathogens that infect plants.
Their presence can have a severe impact on the agriculture industry.
ART CONNECTION QUESTIONS
1. Figure 21.4 Which of the following statements about
virus structure is true?
a. All viruses are encased in a viral membrane.
b. The capsomere is made up of small protein
subunits called capsids.
c. DNA is the genetic material in all viruses.
d. Glycoproteins help the virus attach to the host
cell.
2. Figure 21.8 Influenza virus is packaged in a viral
envelope that fuses with the plasma membrane. This way,
the virus can exit the host cell without killing it. What
advantage does the virus gain by keeping the host cell
alive?
3. Figure 21.10 Which of the following statements is
false?
a. In the lytic cycle, new phage are produced and
released into the environment.
b. In the lysogenic cycle, phage DNA is
incorporated into the host genome.
c. An environmental stressor can cause the phage
to initiate the lysogenic cycle.
d. Cell lysis only occurs in the lytic cycle.
REVIEW QUESTIONS
4. Which statement is true?
a. A virion contains DNA and RNA.
b. Viruses are acellular.
c. Viruses replicate outside of the cell.
d. Most viruses are easily visualized with a light
microscope.
5. The viral ________ plays a role in attaching a virion to
the host cell.
a. core
b. capsid
c. envelope
d. both b and c
6. Viruses_______.
a. all have a round shape
b. cannot have a long shape
c. do not maintain any shape
d. vary in shape
7. Which statement is not true of viral replication?
a. A lysogenic cycle kills the host cell.
b. There are six basic steps in the viral replication
cycle.
c. Viral replication does not affect host cell
function.
d. Newly released virions can infect adjacent cells.
8. Which statement is true of viral replication?
a. In the process of apoptosis, the cell survives.
b. During attachment, the virus attaches at specific
sites on the cell surface.
c. The viral capsid helps the host cell produce more
copies of the viral genome.
560 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 d. mRNA works outside of the host cell to produce
enzymes and proteins.
9. Which statement is true of reverse transcriptase?
a. It is a nucleic acid.
b. It infects cells.
c. It transcribes RNA to make DNA.
d. It is a lipid.
10. Oncogenic virus cores can be_______.
a. RNA
b. DNA
c. neither RNA nor DNA
d. either RNA or DNA
11. Which is true of DNA viruses?
a. They use the host cell’s machinery to produce
new copies of their genome.
b. They all have envelopes.
c. They are the only kind of viruses that can cause
cancer.
d. They are not important plant pathogens.
12. A bacteriophage can infect ________.
a. the lungs
b. viruses
c. prions
d. bacteria
13. Which of the following is NOT used to treat active
viral disease?
a. vaccines
b. antiviral drugs
c. antibiotics
d. phage therapy
14. Vaccines_______.
a. are similar to viroids
b. are only needed once
c. kill viruses
d. stimulate an immune response
15. Which of the following is not associated with prions?
a. replicating shapes
b. mad cow disease
c. DNA
d. toxic proteins
16. Which statement is true of viroids?
a. They are single-stranded RNA particles.
b. They reproduce only outside of the cell.
c. They produce proteins.
d. They affect both plants and animals.
CRITICAL THINKING QUESTIONS
17. The first electron micrograph of a virus (tobacco
mosaic virus) was produced in 1939. Before that time,
how did scientists know that viruses existed if they could
not see them? (Hint: Early scientists called viruses
“filterable agents.”)
18. Why can’t dogs catch the measles?
19. One of the first and most important targets for drugs to
fight infection with HIV (a retrovirus) is the reverse
transcriptase enzyme. Why?
20. In this section, you were introduced to different types
of viruses and viral diseases. Briefly discuss the most
interesting or surprising thing you learned about viruses.
21. Although plant viruses cannot infect humans, what are
some of the ways in which they affect humans?
22. Why is immunization after being bitten by a rabid
animal so effective and why aren’t people vaccinated for
rabies like dogs and cats are?
23. Prions are responsible for variant Creutzfeldt-Jakob
Disease, which has resulted in over 100 human deaths in
Great Britain during the last 10 years. How do humans
obtain this disease?
24. How are viroids like viruses?
Chapter 21 | Viruses 561 562 Chapter 21 | Viruses
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 22 | PROKARYOTES:
BACTERIA AND
ARCHAEA
Figure 22.1 Certain prokaryotes can live in extreme environments such as the Morning Glory pool, a hot spring in
Yellowstone National Park. The spring’s vivid blue color is from the prokaryotes that thrive in its very hot waters. (credit:
modification of work by Jon Sullivan)
Chapter Outline
22.1: Prokaryotic Diversity
22.2: Structure of Prokaryotes
22.3: Prokaryotic Metabolism
22.4: Bacterial Diseases in Humans
22.5: Beneficial Prokaryotes
Introduction
In the recent past, scientists grouped living things into five kingdoms—animals, plants, fungi, protists, and
prokaryotes—based on several criteria, such as the absence or presence of a nucleus and other membrane-bound organelles,
the absence or presence of cell walls, multicellularity, and so on. In the late 20 thcentury, the pioneering work of Carl Woese
and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental
way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his
colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all
organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya
comprises all eukaryotes—including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.
Two of the three domains—Bacteria and Archaea—are prokaryotic. Prokaryotes were the first inhabitants on Earth,
appearing 3.5 to 3.8 billion years ago. These organisms are abundant and ubiquitous; that is, they are present everywhere.
Chapter 22 | Prokaryotes: Bacteria and Archaea 563 In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently
frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure,
such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively
contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible
for certain illnesses, and serve an important role in the preparation of many foods.
22.1 | Prokaryotic Diversity
By the end of this section, you will be able to:
• Describe the evolutionary history of prokaryotes
• Discuss the distinguishing features of extremophiles
• Explain why it is difficult to culture prokaryotes
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and
inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one.
They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable
for most living things. Prokaryotes recycle nutrients —essential substances (such as carbon and nitrogen)—and they drive
the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since
long before multicellular life appeared.
Prokaryotes, the First Inhabitants of Earth
When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life
on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be
about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with
other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular
oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where
they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic
activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high
temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by
mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.
Microbial Mats
Microbial mats or large biofilms may represent the earliest forms of life on Earth; there is fossil evidence of their presence
starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes ( Figure 22.2 ) that includes
mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types
of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different
metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a
glue-like sticky substance that they secrete called extracellular matrix.
The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal
vent is a breakage or fissure in the Earth’s surface that releases geothermally heated water. With the evolution of
photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely available energy
source—sunlight—whereas others were still dependent on chemicals from hydrothermal vents for energy and food.
564 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.2 This (a) microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean
in a region known as the “Pacific Ring of Fire.” The mat helps retain microbial nutrients. Chimneys such as the
one indicated by the arrow allow gases to escape. (b) In this micrograph, bacteria are visualized using fluorescence
microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; credit b: modification of
work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)
Stromatolites
Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed
when minerals are precipitated out of water by prokaryotes in a microbial mat ( Figure 22.3 ). Stromatolites form layered
rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where
stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park
in San Diego County, California.
Figure 22.3 (a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found
in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; credit b: P. Carrara, NPS)
The Ancient Atmosphere
Evidence indicates that during the first two billion years of Earth’s existence, the atmosphere was anoxic , meaning that there
was no molecular oxygen. Therefore, only those organisms that can grow without oxygen— anaerobic organisms—were
able to live. Autotrophic organisms that convert solar energy into chemical energy are called phototrophs , and they
appeared within one billion years of the formation of Earth. Then, cyanobacteria , also known as blue-green algae,
evolved from these simple phototrophs one billion years later. Cyanobacteria ( Figure 22.4 ) began the oxygenation of the
atmosphere. Increased atmospheric oxygen allowed the development of more efficient O 2-utilizing catabolic pathways. It
also opened up the land to increased colonization, because some O 2is converted into O 3(ozone) and ozone effectively
absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O 2
concentrations allowed the evolution of other life forms.
Chapter 22 | Prokaryotes: Bacteria and Archaea 565 Figure 22.4 This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are
green, and as water flows down the gradient, the intensity of the color increases as cell density increases. The water
is cooler at the edges of the stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-
Mariño)
Microbes Are Adaptable: Life in Moderate and Extreme Environments
Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array
of environments: Some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow
under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall, a protective structure that allows
them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist
heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with
others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.
Other bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles , meaning “lovers of
extremes.” Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Artic and
the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments
(Figure 22.5 ), just to mention a few. These organisms give us a better understanding of prokaryotic diversity and open up
the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial
applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles
cannot survive in moderate environments. There are many different groups of extremophiles: They are identified based on
the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is
both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles ( Table 22.1 ). Other
extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of
radiation), but have adapted to survive in it ( Figure 22.5 ).
Extremophiles and Their Preferred Conditions
Extremophile Type Conditions for Optimal Growth
Acidophiles pH 3 or below
Alkaliphiles pH 9 or above
Thermophiles Temperature 60–80 °C (140–176 °F)
Hyperthermophiles Temperature 80–122 °C (176–250 °F)
Psychrophiles Temperature of -15-10 °C (5-50 °F) or lower
Halophiles Salt concentration of at least 0.2 M
Osmophiles High sugar concentration
Table 22.1
566 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.5 Deinococcus radiodurans , visualized in this false color transmission electron micrograph, is a prokaryote
that can tolerate very high doses of ionizing radiation. It has developed DNA repair mechanisms that allow it to
reconstruct its chromosome even if it has been broken into hundreds of pieces by radiation or heat. (credit: modification
of work by Michael Daly; scale-bar data from Matt Russell)
Prokaryotes in the Dead Sea
One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel.
Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times
higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater)
that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe 2+,Ca 2+, and
Mg 2+), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations,
the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem [1]
(Figure 22.6 ).
What sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include Halobacterium ,
Haloferax volcanii (which is found in other locations, not only the Dead Sea), Halorubrum sodomense , and Halobaculum
gomorrense , and the archaea Haloarcula marismortui , among others.
Figure 22.6 (a) The Dead Sea is hypersaline. Nevertheless, salt-tolerant bacteria thrive in this sea. (b) These
halobacteria cells can form salt-tolerant bacterial mats. (credit a: Julien Menichini; credit b: NASA; scale-bar data from
Matt Russell)
Unculturable Prokaryotes and the Viable-but-Non-Culturable State
Microbiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the
nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right
temperature, there should be evidence of microbial growth ( Figure 22.7 ). The process of culturing bacteria is complex
1. Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the DeadSea: An increasingly extreme environment. The ISME Journal 4 (2010): 399–407, doi:10.1038/ismej.2009.141 . published online 24 December 2009.
Chapter 22 | Prokaryotes: Bacteria and Archaea 567 and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the
techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish
whose use persists in today’s laboratories. Koch worked primarily with the Mycobacterium tuberculosis bacterium that
causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the
medical community. Koch’s postulates include that an organism can be identified as the cause of disease when it is present in
all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple
times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.
Figure 22.7 In these agar plates, the growth medium is supplemented with red blood cells. Blood agar becomes
transparent in the presence of hemolytic Streptococcus , which destroys red blood cells and is used to diagnose
Streptococcus infections. The plate on the left is inoculated with non-hemolytic Staphylococcus (large white colonies),
and the plate on the right is inoculated with hemolytic Streptococcus (tiny clear colonies). If you look closely at the right
plate, you can see that the agar surrounding the bacteria has turned clear. (credit: Bill Branson, NCI)
Some prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are
unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them;
they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH,
temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular
parasites and cannot be grown outside a host cell.
In other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could
be cultured previously. Those organisms that cannot be cultured but are not dead are in a viable-but-non-culturable
(VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state
that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called
resuscitation , the prokaryote can go back to “normal” life when environmental conditions improve.
Is the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic
waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured
under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive?
Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of
DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a
process called amplification.
The Ecology of Biofilms
Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model,
however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can
interact. A biofilm is a microbial community ( Figure 22.8 ) held together in a gummy-textured matrix that consists primarily
of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to
surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described
as well as some composed of a mixture of fungi and bacteria.
Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial
settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also
colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human
body, such as the surfaces of our teeth.
Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS)
environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance
that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their
568 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of
sterilization.
Figure 22.8 Five stages of biofilm development are shown. During stage 1, initial attachment, bacteria adhere to
a solid surface via weak van der Waals interactions. During stage 2, irreversible attachment, hairlike appendages
called pili permanently anchor the bacteria to the surface. During stage 3, maturation I, the biofilm grows through
cell division and recruitment of other bacteria. An extracellular matrix composed primarily of polysaccharides
holds the biofilm together. During stage 4, maturation II, the biofilm continues to grow and takes on a more
complex shape. During stage 5, dispersal, the biofilm matrix is partly broken down, allowing some bacteria to
escape and colonize another surface. Micrographs of a Pseudomonas aeruginosa biofilm in each of the stages of
development are shown. (credit: D. Davis, Don Monroe, PLoS)
Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and
detergents. Why do you think this might be the case?
22.2 | Structure of Prokaryotes
By the end of this section, you will be able to:
• Describe the basic structure of a typical prokaryote
• Describe important differences in structure between Archaea and Bacteria
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the
plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a
jelly-like substance inside the cell; nucleic acids, the genetic material of the cell; and ribosomes, where protein synthesis
takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped),
and spirilli (spiral-shaped) ( Figure 22.9 ).
Chapter 22 | Prokaryotes: Bacteria and Archaea 569 Figure 22.9 Prokaryotes fall into three basic categories based on their shape, visualized here using scanning electron
microscopy: (a) cocci, or spherical (a pair is shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral-shaped. (credit
a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit c: modification of work by Dr. David
Cox; scale-bar data from Matt Russell)
The Prokaryotic Cell
Recall that prokaryotes ( Figure 22.10 ) are unicellular organisms that lack organelles or other internal membrane-bound
structures. Therefore, they do not have a nucleus but instead generally have a single chromosome—a piece of circular,
double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma
membrane.
Figure 22.10 The features of a typical prokaryotic cell are shown.
Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya,
comprise the three domains of life ( Figure 22.11 ).
570 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.11 Bacteria and Archaea are both prokaryotes but differ enough to be placed in separate domains. An
ancestor of modern Archaea is believed to have given rise to Eukarya, the third domain of life. Archaeal and bacterial
phyla are shown; the evolutionary relationship between these phyla is still open to debate.
The composition of the cell wall differs significantly between the domains Bacteria and Archaea. The composition of
their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin). The cell
wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacteria have an outer capsule
outside the cell wall. Other structures are present in some prokaryotic species, but not in others ( Table 22.2 ). For example,
the capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by
phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular,
flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces. Plasmids, which consist of extra-
chromosomal DNA, are also present in many species of bacteria and archaea.
Characteristics of phyla of Bacteria are described in Figure 22.12 and Figure 22.13 ; Archaea are described in Figure 22.14 .
Chapter 22 | Prokaryotes: Bacteria and Archaea 571 Figure 22.12 Phylum Proteobacteria is one of up to 52 bacteria phyla. Proteobacteria is further subdivided into five
classes, Alpha through Epsilon. (credit “Rickettsia rickettsia”: modification of work by CDC; credit “Spirillum minus”:
modification of work by Wolframm Adlassnig; credit “Vibrio cholera”: modification of work by Janice Haney Carr, CDC;
credit “Desulfovibrio vulgaris”: modification of work by Graham Bradley; credit “Campylobacter”: modification of work
by De Wood, Pooley, USDA, ARS, EMU; scale-bar data from Matt Russell)
572 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.13 Chlamydia, Spirochetes, Cyanobacteria, and Gram-positive bacteria are described in this table. Note
that bacterial shape is not phylum-dependent; bacteria within a phylum may be cocci, rod-shaped, or spiral. (credit
“Chlamydia trachomatis”: modification of work by Dr. Lance Liotta Laboratory, NCI; credit “Treponema pallidum”:
modification of work by Dr. David Cox, CDC; credit “Phormidium”: modification of work by USGS; credit “Clostridium
difficile”: modification of work by Lois S. Wiggs, CDC; scale-bar data from Matt Russell)
Chapter 22 | Prokaryotes: Bacteria and Archaea 573 Figure 22.14 Archaea are separated into four phyla: the Korarchaeota, Euryarchaeota, Crenarchaeota, and
Nanoarchaeota. (credit “Halobacterium”: modification of work by NASA; credit “Nanoarchaeotum equitans”:
modification of work by Karl O. Stetter; credit “korarchaeota”: modification of work by Office of Science of the U.S.
Dept. of Energy; scale-bar data from Matt Russell)
The Plasma Membrane
The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside
from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them
from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the
general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell
membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes.
Some archaeal membranes are lipid monolayers instead of bilayers ( Figure 22.14 ).
574 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.15 Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have
branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the
lipid to the glycerol.
The Cell Wall
The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within
the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity.
It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical
composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.
Bacterial cell walls contain peptidoglycan , composed of polysaccharide chains that are cross-linked by unusual peptides
containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino
acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on
bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins
are also present on the outside of cell walls of both archaea and bacteria.
Bacteria are divided into two major groups: Gram positive and Gram negative , based on their reaction to Gram staining.
Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias,
Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish
scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to
cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms ( Figure
22.15 ). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest
is composed of acidic substances called teichoic acids . Teichoic acids may be covalently linked to lipids in the plasma
membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria
have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded
by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as
a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer
that forms plasma membranes.
Chapter 22 | Prokaryotes: Bacteria and Archaea 575 Figure 22.16 Bacteria are divided into two major groups: Gram positive and Gram negative. Both groups have
a cell wall composed of peptidoglycan: in Gram-positive bacteria, the wall is thick, whereas in Gram-negative
bacteria, the wall is thin. In Gram-negative bacteria, the cell wall is surrounded by an outer membrane that
contains lipopolysaccharides and lipoproteins. Porins are proteins in this cell membrane that allow substances to
pass through the outer membrane of Gram-negative bacteria. In Gram-positive bacteria, lipoteichoic acid anchors
the cell wall to the cell membrane. (credit: modification of work by "Franciscosp2"/Wikimedia Commons)
Which of the following statements is true?
a. Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
b. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
c. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
d. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have
a cell wall made of lipoteichoic acid.
Archaean cell walls do not have peptidoglycan. There are four different types of Archaean cell walls. One type is
composed of pseudopeptidoglycan , which is similar to peptidoglycan in morphology but contains different sugars in the
polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein.
Structural Differences and Similarities between Bacteria and Archaea
Structural Characteristic Bacteria Archaea
Cell type Prokaryotic Prokaryotic
Cell morphology Variable Variable
Cell wall Contains peptidoglycan Does not contain peptidoglycan
Cell membrane type Lipid bilayer Lipid bilayer or lipid monolayer
Plasma membrane lipids Fatty acids Phytanyl groups
Table 22.2
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote exists
as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather the chromosome is replicated and the two
resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at
its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic
recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.
576 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 In transformation , the prokaryote takes in DNA found in its environment that is shed by other prokaryotes. If a
nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own
chromosome, it too may become pathogenic. In transduction , bacteriophages, the viruses that infect bacteria, sometimes
also move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant
organism. Archaea are not affected by bacteriophages but instead have their own viruses that translocate genetic material
from one individual to another. In conjugation , DNA is transferred from one prokaryote to another by means of a pilus,
which brings the organisms into contact with one another. The DNA transferred can be in the form of a plasmid or as a
hybrid, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure
22.17 .
Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of
genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to
environmental changes (such as the introduction of an antibiotic) very quickly.
Figure 22.17 Besides binary fission, there are three other mechanisms by which prokaryotes can exchange DNA. In
(a) transformation, the cell takes up prokaryotic DNA directly from the environment. The DNA may remain separate as
plasmid DNA or be incorporated into the host genome. In (b) transduction, a bacteriophage injects DNA into the cell
that contains a small fragment of DNA from a different prokaryote. In (c) conjugation, DNA is transferred from one cell
to another via a mating bridge that connects the two cells after the sex pilus draws the two bacteria close enough to
form the bridge.
Chapter 22 | Prokaryotes: Bacteria and Archaea 577 The Evolution of Prokaryotes
How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in
the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny
bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds
that the more recently two species have diverged, the more similar their genes (and thus proteins) will be.
Conversely, species that diverged long ago will have more genes that are dissimilar.
Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory
collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of
prokaryotes. [2] The model they derived from their data indicates that three important groups of
bacteria—Actinobacteria, Deinococcus , and Cyanobacteria (which the authors call Terrabacteria )—were
the first to colonize land. (Recall that Deinococcus is a genus of prokaryote—a bacterium—that is highly
resistant to ionizing radiation.) Cyanobacteria are photosynthesizers, while Actinobacteria are a group of
very common bacteria that include species important in decomposition of organic wastes.
The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common
ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1
and 4.1 billion years ago. Eukarya later diverged off the Archaean line. The work further suggests that
stromatolites that formed prior to the advent of cyanobacteria (about 2.6 billion years ago) photosynthesized
in an anoxic environment and that because of the modifications of the Terrabacteria for land (resistance to
drying and the possession of compounds that protect the organism from excess light), photosynthesis using
oxygen may be closely linked to adaptations to survive on land.
22.3 | Prokaryotic Metabolism
By the end of this section, you will be able to:
• Identify the macronutrients needed by prokaryotes, and explain their importance
• Describe the ways in which prokaryotes get energy and carbon for life processes
• Describe the roles of prokaryotes in the carbon and nitrogen cycles
Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and
carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy
and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such
as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The
very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.
Needs of Prokaryotes
The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available
nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of
nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.
Macronutrients
Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced
by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they
need certain substances, collectively called nutrients . When prokaryotes grow in nature, they obtain their nutrients from
the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller
2. Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, andthe colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.
578 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen,
oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS .)
Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including
water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other
compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total
dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen
available in nature is either atmospheric nitrogen (N 2) or another inorganic form. Diatomic (N 2) nitrogen, however, can
be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen
are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides
and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present
in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca),
and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and
function of the prokaryotic cell.
Micronutrients
In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred
to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in
electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese
(Mn)—primarily as enzyme cofactors.
The Ways in Which Prokaryotes Obtain Energy
Prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs
(or phototrophic organisms) obtain their energy from sunlight. Chemotrophs (or chemosynthetic organisms) obtain
their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called
chemoorganotrophs. Those that can also use inorganic compounds as energy sources are called chemolitotrophs.
The Ways in Which Prokaryotes Obtain Carbon
Prokaryotes not only can use different sources of energy but also different sources of carbon compounds. Recall that
organisms that are able to fix inorganic carbon are called autotrophs. Autotrophic prokaryotes synthesize organic molecules
from carbon dioxide. In contrast, heterotrophic prokaryotes obtain carbon from organic compounds. To make the picture
more complex, the terms that describe how prokaryotes obtain energy and carbon can be combined. Thus, photoautotrophs
use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon
from an organic chemical source. Chemolitoautotrophs obtain their energy from inorganic compounds, and they build
their complex molecules from carbon dioxide. The table below ( Table 22.3 ) summarizes carbon and energy sources in
prokaryotes.
Carbon and Energy Sources in Prokaryotes
Energy Sources Carbon Sources
Light Chemicals Carbon dioxide Organic compounds
Phototrophs Chemotrophs Autotrophs Heterotrophs
Organic chemicals Inorganic chemicals
Chemo-organotrophs Chemolithotrophs
Table 22.3
Role of Prokaryotes in Ecosystems
Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in
the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth.
Prokaryotes and the Carbon Cycle
Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle ( Figure
22.18 ). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks,
and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and
marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including
Chapter 22 | Prokaryotes: Bacteria and Archaea 579 prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments,
that carbon is not readily available.
A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air
to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is
a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as
animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and
fungi, collectively called decomposers , carry out the breakdown (decomposition) of plants and animals and their organic
compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead
material (dead animals, plants, and humus) that undergo respiration.
In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is
based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH 4). This methane
moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that
oxidize methane to carbon dioxide, which then returns to the atmosphere.
Figure 22.18 Prokaryotes play a significant role in continuously moving carbon through the biosphere. (credit:
modification of work by John M. Evans and Howard Perlman, USGS)
Prokaryotes and the Nitrogen Cycle
Nitrogen is a very important element for life because it is part of proteins and nucleic acids. It is a macronutrient, and in
nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by myriad
processes, many of which are carried out only by prokaryotes. As illustrated in Figure 22.19 , prokaryotes are key to the
nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this
nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed” into more readily
available forms such as ammonia through the process of nitrogen fixation . Ammonia can be used by plants or converted to
other forms.
Another source of ammonia is ammonification , the process by which ammonia is released during the decomposition of
nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the
total nitrogen released; the rest is as N 2and N 2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N 2
as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out
by bacteria belonging to the genera Nitrosomas ,Nitrobacter , and Nitrospira . The bacteria performs the reverse process, the
reduction of nitrate from the soils to gaseous compounds such as N 2O, NO, and N 2, a process called denitrification .
580 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.19 Prokaryotes play a key role in the nitrogen cycle. (credit: Environmental Protection Agency)
Which of the following statements about the nitrogen cycle is false?
a. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
b. Denitrifying bacteria convert nitrates (NO 3-) into nitrogen gas (N 2).
c. Ammonification is the process by which ammonium ion (NH 4+) is released from decomposing organic
compounds.
d. Nitrification is the process by which nitrites (NO 2-) are converted to ammonium ion (NH 4+).
22.4 | Bacterial Diseases in Humans
By the end of this section, you will be able to:
• Identify bacterial diseases that caused historically important plagues and epidemics
• Describe the link between biofilms and foodborne diseases
• Explain how overuse of antibiotic may be creating “super bugs”
• Explain the importance of MRSA with respect to the problems of antibiotic resistance
Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected humans since the
beginning of human history. The true cause of these diseases was not understood at the time, and some people thought
that diseases were a spiritual punishment. Over time, people came to realize that staying apart from afflicted persons, and
disposing of the corpses and personal belongings of victims of illness, reduced their own chances of getting sick.
Epidemiologists study how diseases affect a population. An epidemic is a disease that occurs in an unusually high number
of individuals in a population at the same time. A pandemic is a widespread, usually worldwide, epidemic. An endemic
disease is a disease that is constantly present, usually at low incidence, in a population.
Chapter 22 | Prokaryotes: Bacteria and Archaea 581 Long History of Bacterial Disease
There are records about infectious diseases as far back as 3000 B.C. A number of significant pandemics caused by bacteria
have been documented over several hundred years. Some of the most memorable pandemics led to the decline of cities and
nations.
In the 21 stcentury, infectious diseases remain among the leading causes of death worldwide, despite advances made in
medical research and treatments in recent decades. A disease spreads when the pathogen that causes it is passed from one
person to another. For a pathogen to cause disease, it must be able to reproduce in the host’s body and damage the host in
some way.
The Plague of Athens
In 430 B.C., the Plague of Athens killed one-quarter of the Athenian troops that were fighting in the great Peloponnesian
War and weakened Athens’ dominance and power. The plague impacted people living in overcrowded Athens as well
as troops aboard ships that had to return to Athens. The source of the plague may have been identified recently when
researchers from the University of Athens were able to use DNA from teeth recovered from a mass grave. The scientists
identified nucleotide sequences from a pathogenic bacterium, Salmonella enterica serovar Typhi ( Figure 22.20 ), which
causes typhoid fever. [
This disease is commonly seen in overcrowded areas and has caused epidemics throughout recorded
history.
Figure 22.20 Salmonella enterica serovar Typhi, the causative agent of Typhoid fever, is a Gram-negative, rod-
shaped gamma protobacterium. Typhoid fever, which is spread through feces, causes intestinal hemorrhage, high
fever, delirium and dehydration. Today, between 16 and 33 million cases of this re-emerging disease occur annually,
resulting in over 200,000 deaths. Carriers of the disease can be asymptomatic. In a famous case in the early 1900s, a
cook named Mary Mallon unknowingly spread the disease to over fifty people, three of whom died. Other Salmonella
serotypes cause food poisoning. (credit: modification of work by NCI, CDC)
Bubonic Plagues
From 541 to 750, an outbreak of what was likely a bubonic plague (the Plague of Justinian), eliminated one-quarter to one-
half of the human population in the eastern Mediterranean region. The population in Europe dropped by 50 percent during
this outbreak. Bubonic plague would strike Europe more than once.
One of the most devastating pandemics was the Black Death (1346 to 1361) that is believed to have been another outbreak
of bubonic plague caused by the bacterium Yersinia pestis . It is thought to have originated initially in China and spread
along the Silk Road, a network of land and sea trade routes, to the Mediterranean region and Europe, carried by rat fleas
living on black rats that were always present on ships. The Black Death reduced the world’s population from an estimated
450 million to about 350 to 375 million. Bubonic plague struck London hard again in the mid-1600s ( Figure 22.21 ). In
modern times, approximately 1,000 to 3,000 cases of plague arise globally each year. Although contracting bubonic plague
before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, and mortality
rates from plague are now very low.
3. Papagrigorakis MJ , Synodinos PN , and Yapijakis C . Ancient typhoid epidemic reveals possible ancestral strain of Salmonella enterica serovar Typhi. Infect Genet Evol 7 (2007): 126–7, Epub 2006 Jun.
582 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.21 The (a) Great Plague of London killed an estimated 200,000 people, or about twenty percent of the city’s
population. The causative agent, the (b) bacterium Yersinia pestis , is a Gram-negative, rod-shaped bacterium from
the class Gamma Proteobacteria. The disease is transmitted through the bite of an infected flea, which is infected
by a rodent. Symptoms include swollen lymph nodes, fever, seizure, vomiting of blood, and (c) gangrene. (credit b:
Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt Russell; credit c: Textbook of Military Medicine,
Washington, D.C., U.S. Dept. of the Army, Office of the Surgeon General, Borden Institute)
Wa t c h a video (http://openstaxcollege.org/l/black_death) on the modern understanding of the Black Death—bubonic
plague in Europe during the 14 thcentury.
Migration of Diseases to New Populations
Over the centuries, Europeans tended to develop genetic immunity to endemic infectious diseases, but when European
conquerors reached the western hemisphere, they brought with them disease-causing bacteria and viruses, which triggered
epidemics that completely devastated populations of Native Americans, who had no natural resistance to many European
diseases. It has been estimated that up to 90 percent of Native Americans died from infectious diseases after the arrival of
Europeans, making conquest of the New World a foregone conclusion.
Emerging and Re-emerging Diseases
The distribution of a particular disease is dynamic. Therefore, changes in the environment, the pathogen, or the host
population can dramatically impact the spread of a disease. According to the World Health Organization (WHO) an
emerging disease (Figure 22.22 ) is one that has appeared in a population for the first time, or that may have existed
previously but is rapidly increasing in incidence or geographic range. This definition also includes re-emerging diseases
that were previously under control. Approximately 75 percent of recently emerging infectious diseases affecting humans are
zoonotic diseases, zoonoses , diseases that primarily infect animals and are transmitted to humans; some are of viral origin
and some are of bacterial origin. Brucellosis is an example of a prokaryotic zoonosis that is re-emerging in some regions,
and necrotizing fasciitis (commonly known as flesh-eating bacteria) has been increasing in virulence for the last 80 years
for unknown reasons.
Chapter 22 | Prokaryotes: Bacteria and Archaea 583 Figure 22.22 The map shows regions where bacterial diseases are emerging or reemerging. (credit: modification of
work by NIH)
Some of the present emerging diseases are not actually new, but are diseases that were catastrophic in the past ( Figure
22.23 ). They devastated populations and became dormant for a while, just to come back, sometimes more virulent than
before, as was the case with bubonic plague. Other diseases, like tuberculosis, were never eradicated but were under control
in some regions of the world until coming back, mostly in urban centers with high concentrations of immunocompromised
people. The WHO has identified certain diseases whose worldwide re-emergence should be monitored. Among these are
two viral diseases (dengue fever and yellow fever), and three bacterial diseases (diphtheria, cholera, and bubonic plague).
The war against infectious diseases has no foreseeable end.
Figure 22.23 Lyme disease often, but not always, results in (a) a characteristic bullseye rash. The disease is caused by
a (b) Gram-negative spirochete bacterium of the genus Borrelia . The bacteria (c) infect ticks, which in turns infect mice.
Deer are the preferred secondary host, but the ticks also may feed on humans. Untreated, the disease causes chronic
disorders in the nervous system, eyes, joints, and heart. The disease is named after Lyme, Connecticut, where an
outbreak occurred in 1995 and has subsequently spread. The disease is not new, however. Genetic evidence suggests
that Ötzi the Iceman, a 5,300-year-old mummy found in the Alps, was infected with Borrelia . (credit a: James Gathany,
CDC; credit b: CDC; scale-bar data from Matt Russell)
Biofilms and Disease
Recall that biofilms are microbial communities that are very difficult to destroy. They are responsible for diseases such as
infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque and colonize
catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers.
They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines,
mechanical ventilators, shunts, and other medical equipment. In fact, 65 percent of all infections acquired in the hospital
(nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they
colonize the surfaces of vegetable leaves and meat, as well as food-processing equipment that isn’t adequately cleaned.
Biofilm infections develop gradually; sometimes, they do not cause symptoms immediately. They are rarely resolved by
host defense mechanisms. Once an infection by a biofilm is established, it is very difficult to eradicate, because biofilms
584 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 tend to be resistant to most of the methods used to control microbial growth, including antibiotics. Biofilms respond poorly
or only temporarily to antibiotics; it has been said that they can resist up to 1,000 times the antibiotic concentrations used
to kill the same bacteria when they are free-living or planktonic. An antibiotic dose that large would harm the patient;
therefore, scientists are working on new ways to get rid of biofilms.
Antibiotics: Are We Facing a Crisis?
The word antibiotic comes from the Greek anti meaning “against” and bios meaning “life.” An antibiotic is a chemical,
produced either by microbes or synthetically, that is hostile to the growth of other organisms. Today’s news and media often
address concerns about an antibiotic crisis. Are the antibiotics that easily treated bacterial infections in the past becoming
obsolete? Are there new “superbugs”—bacteria that have evolved to become more resistant to our arsenal of antibiotics? Is
this the beginning of the end of antibiotics? All these questions challenge the healthcare community.
One of the main causes of resistant bacteria is the abuse of antibiotics. The imprudent and excessive use of antibiotics
has resulted in the natural selection of resistant forms of bacteria. The antibiotic kills most of the infecting bacteria, and
therefore only the resistant forms remain. These resistant forms reproduce, resulting in an increase in the proportion of
resistant forms over non-resistant ones. Another major misuse of antibiotics is in patients with colds or the flu, for which
antibiotics are useless. Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in
animal feed promotes bacterial resistance as well. In the United States, 70 percent of the antibiotics produced are fed to
animals. These antibiotics are given to livestock in low doses, which maximize the probability of resistance developing, and
these resistant bacteria are readily transferred to humans.
Watch a recent news report (http://openstaxcollege.org/l/antibiotics) on the problem of routine antibiotic
administration to livestock and antibiotic-resistant bacteria.
One of the Superbugs: MRSA
The imprudent use of antibiotics has paved the way for bacteria to expand populations of resistant forms. For example,
Staphylococcus aureu s, often called “staph,” is a common bacterium that can live in the human body and is usually
easily treated with antibiotics. A very dangerous strain, however, methicillin-resistant Staphylococcus aureus (MRSA)
has made the news over the past few years ( Figure 22.24 ). This strain is resistant to many commonly used antibiotics,
including methicillin, amoxicillin, penicillin, and oxacillin. MRSA can cause infections of the skin, but it can also
infect the bloodstream, lungs, urinary tract, or sites of injury. While MRSA infections are common among people in
healthcare facilities, they have also appeared in healthy people who haven’t been hospitalized but who live or work in tight
populations (like military personnel and prisoners). Researchers have expressed concern about the way this latter source
of MRSA targets a much younger population than those residing in care facilities. The Journal of the American Medical
Association reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68, whereas people
with “community-associated MRSA” ( CA-MRSA ) have an average age of 23. [4]
4. Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community- and health care-associated methicillin-resistant Staphylococcus aureus infection. JAMA 290 (2003): 2976–84, doi: 10.1001/jama.290.22.2976 .
Chapter 22 | Prokaryotes: Bacteria and Archaea 585 Figure 22.24 This scanning electron micrograph shows methicillin-resistant Staphylococcus aureus bacteria,
commonly known as MRSA. S. aureus is not always pathogenic, but can cause diseases such as food poisoning and
skin and respiratory infections. (credit: modification of work by Janice Haney Carr; scale-bar data from Matt Russell)
In summary, the medical community is facing an antibiotic crisis. Some scientists believe that after years of being protected
from bacterial infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again
devastate the human population. Researchers are developing new antibiotics, but it takes many years to of research and
clinical trials, plus financial investments in the millions of dollars, to generate an effective and approved drug.
Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Most of
the time, prokaryotes colonize food and food-processing equipment in the form of a biofilm. Outbreaks of bacterial infection
related to food consumption are common. A foodborne disease (colloquially called “food poisoning”) is an illness resulting
from the consumption the pathogenic bacteria, viruses, or other parasites that contaminate food. Although the United States
has one of the safest food supplies in the world, the U.S. Centers for Disease Control and Prevention (CDC) has reported
that “76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne
illness.”
The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear about
sporadic cases of botulism , the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium
botulinum . Some of the most common sources for this bacterium were non-acidic canned foods, homemade pickles, and
processed meat and sausages. The can, jar, or package created a suitable anaerobic environment where Clostridium could
grow. Proper sterilization and canning procedures have reduced the incidence of this disease.
While people may tend to think of foodborne illnesses as associated with animal-based foods, most cases are now linked
to produce. There have been serious, produce-related outbreaks associated with raw spinach in the United States and with
vegetable sprouts in Germany, and these types of outbreaks have become more common. The raw spinach outbreak in
2006 was produced by the bacterium E. coli serotype O157:H7. A serotype is a strain of bacteria that carries a set of
similar antigens on its cell surface, and there are often many different serotypes of a bacterial species. Most E. coli are not
particularly dangerous to humans, but serotype O157:H7 can cause bloody diarrhea and is potentially fatal.
All types of food can potentially be contaminated with bacteria. Recent outbreaks of Salmonella reported by the CDC
occurred in foods as diverse as peanut butter, alfalfa sprouts, and eggs. A deadly outbreak in Germany in 2010 was caused
by E. coli contamination of vegetable sprouts ( Figure 22.25 ). The strain that caused the outbreak was found to be a new
serotype not previously involved in other outbreaks, which indicates that E. coli is continuously evolving.
586 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.25 (a) Vegetable sprouts grown at an organic farm were the cause of an (b) E. coli outbreak that killed
32 people and sickened 3,800 in Germany in 2011. The strain responsible, E. coli O104:H4, produces Shiga toxin,
a substance that inhibits protein synthesis in the host cell. The toxin (c) destroys red blood cells resulting in bloody
diarrhea. Deformed red blood cells clog the capillaries of the kidney, which can lead to kidney failure, as happened to
845 patients in the 2011 outbreak. Kidney failure is usually reversible, but some patients experience kidney problems
years later. (credit c: NIDDK, NIH)
Epidemiologist
Epidemiology is the study of the occurrence, distribution, and determinants of health and disease in a
population. It is, therefore, part of public health. An epidemiologist studies the frequency and distribution of
diseases within human populations and environments.
Epidemiologists collect data about a particular disease and track its spread to identify the original mode
of transmission. They sometimes work in close collaboration with historians to try to understand the way
a disease evolved geographically and over time, tracking the natural history of pathogens. They gather
information from clinical records, patient interviews, surveillance, and any other available means. That
information is used to develop strategies, such as vaccinations ( Figure 22.26 ), and design public health
policies to reduce the incidence of a disease or to prevent its spread. Epidemiologists also conduct rapid
investigations in case of an outbreak to recommend immediate measures to control it.
An epidemiologist has a bachelor’s degree, plus a master’s degree in public health (MPH). Many
epidemiologists are also physicians (and have an M.D.), or they have a Ph.D. in an associated field, such
as biology or microbiology.
Figure 22.26 Vaccinations can slow the spread of communicable diseases. (credit: modification of work by Daniel
Paquet)
Chapter 22 | Prokaryotes: Bacteria and Archaea 587 22.5 | Beneficial Prokaryotes
By the end of this section, you will be able to:
• Explain the need for nitrogen fixation and how it is accomplished
• Identify foods in which prokaryotes are used in the processing
• Describe the use of prokaryotes in bioremediation
• Describe the beneficial effects of bacteria that colonize our skin and digestive tracts
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of
the microbial world. In fact, our life would not be possible without prokaryotes. Just think about the role of prokaryotes in
biogeochemical cycles.
Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation
Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the
building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial
ecosystems, with atmospheric nitrogen, N 2, providing the largest pool of available nitrogen. However, eukaryotes cannot
use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is
converted into ammonia (NH 3) either biologically or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or
by industrial processes.
Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia
spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis,
BNF is the second most important biological process on Earth. The equation representing the process is as follows
N2 + 16ATP + 8e − + 8H + → 2NH 3 + 16ADP + 16Pi + H 2
where Pi stands for inorganic phosphate. The total fixed nitrogen through BNF is about 100 to 180 million metric tons per
year. Biological processes contribute 65 percent of the nitrogen used in agriculture.
Cyanobacteria are the most important nitrogen fixers in aquatic environments. In soil, members of the genus Clostridium
are examples of free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with legume plants, providing the
most important source of BNF. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10. Soil
bacteria, collectively called rhizobia, are able to symbiotically interact with legumes to form nodules , specialized structures
where nitrogen fixation occurs ( Figure 22.27 ). Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so
the nodule provides an oxygen-free area for nitrogen fixation to take place. This process provides a natural and inexpensive
plant fertilizer, as it reduces atmospheric nitrogen to ammonia, which is easily usable by plants. The use of legumes is an
excellent alternative to chemical fertilization and is of special interest to sustainable agriculture, which seeks to minimize
the use of chemicals and conserve natural resources. Through symbiotic nitrogen fixation, the plant benefits from using
an endless source of nitrogen: the atmosphere. Bacteria benefit from using photosynthates (carbohydrates produced during
photosynthesis) from the plant and having a protected niche. Additionally, the soil benefits from being naturally fertilized.
Therefore, the use of rhizobia as biofertilizers is a sustainable practice.
Why are legumes so important? Some, like soybeans, are key sources of agricultural protein. Some of the most important
grain legumes are soybean, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.
588 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 22.27 Soybean ( Glycine max ) is a legume that interacts symbiotically with the soil bacterium Bradyrhizobium
japonicum to form specialized structures on the roots called nodules where nitrogen fixation occurs. (credit: USDA)
Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt
According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that
uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific
use." [5]The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection,
antibiotic production, and cell culture are current topics of study in biotechnology. However, humans have used prokaryotes
before the term biotechnology was even coined. In addition, some of the goods and services are as simple as cheese, bread,
wine, beer, and yogurt, which employ both bacteria and other microbes, such as yeast, a fungus ( Figure 22.28 ).
5. http://www.cbd.int/convention/articles/?a=cbd-02, United Nations Convention on Biological Diversity: Article 2: Use of Terms.
Chapter 22 | Prokaryotes: Bacteria and Archaea 589 Figure 22.28 Some of the products derived from the use of prokaryotes in early biotechnology include (a) cheese, (b)
wine, (c) beer and bread, and (d) yogurt. (credit bread: modification of work by F. Rodrigo/Wikimedia Commons; credit
wine: modification of work by Jon Sullivan; credit beer and bread: modification of work by Kris Miller; credit yogurt:
modification of work by Jon Sullivan)
Cheese production began around 4,000–7,000 years ago when humans began to breed animals and process their milk.
Fermentation in this case preserves nutrients: Milk will spoil relatively quickly, but when processed as cheese, it is more
stable. As for beer, the oldest records of brewing are about 6,000 years old and refer to the Sumerians. Evidence indicates
that the Sumerians discovered fermentation by chance. Wine has been produced for about 4,500 years, and evidence
suggests that cultured milk products, like yogurt, have existed for at least 4,000 years.
Using Prokaryotes to Clean up Our Planet: Bioremediation
Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation
has been used to remove agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and the
subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by
bioremediation. The reduction of SeO 4-2to SeO 3-2and to Se 0(metallic selenium) is a method used to remove selenium
ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation.
As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes,
such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it
is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of
toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa , can convert Hg +2 into Hg 0, which is
nontoxic to humans.
One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of
oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent
years, such as the Exxon Valdez spill in Alaska (1989) ( Figure 22.29 ), the Prestige oil spill in Spain (2002), the spill
into the Mediterranean from a Lebanon power plant (2006), and more recently, the BP oil spill in the Gulf of Mexico
(2010). To clean up these spills, bioremediation is promoted by the addition of inorganic nutrients that help bacteria to grow.
Hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplet, breaking down the hydrocarbons. Some species,
such as Alcanivorax borkumensis , produce surfactants that solubilize the oil, whereas other bacteria degrade the oil into
carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are
590 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 oil-consuming bacteria in the ocean prior to the spill. In addition to naturally occurring oil-degrading bacteria, humans select
and engineer bacteria that possess the same capability with increased efficacy and spectrum of hydrocarbon compounds that
can be processed. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can
be degraded within one year of the spill. Other oil fractions containing aromatic and highly branched hydrocarbon chains
are more difficult to remove and remain in the environment for longer periods of time.
Figure 22.29 (a) Cleaning up oil after the Valdez spill in Alaska, workers hosed oil from beaches and then used a
floating boom to corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able
to solubilize and degrade the oil. (b) One of the most catastrophic consequences of oil spills is the damage to fauna.
(credit a: modification of work by NOAA; credit b: modification of work by GOLUBENKOV, NGO: Saving Taman)
Chapter 22 | Prokaryotes: Bacteria and Archaea 591 Microbes on the Human Body
The commensal bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us. They
protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients.
These activities have been known for a long time. More recently, scientists have gathered evidence that
these bacteria may also help regulate our moods, influence our activity levels, and even help control weight
by affecting our food choices and absorption patterns. The Human Microbiome Project has begun the
process of cataloging our normal bacteria (and archaea) so we can better understand these functions.
A particularly fascinating example of our normal flora relates to our digestive systems. People who take
high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-
resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially
chronic diarrhea ( Figure 22.30 ). Obviously, trying to treat this problem with antibiotics only makes it worse.
However, it has been successfully treated by giving the patients fecal transplants from healthy donors to
reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and
effectiveness of this technique.
Figure 22.30 This scanning electron micrograph shows Clostridium difficile , a Gram-positive, rod-shaped
bacterium that causes severe diarrhea. Infection commonly occurs after the normal gut fauna is eradicated by
antibiotics. (credit: modification of work by CDC, HHS; scale-bar data from Matt Russell)
Scientists are also discovering that the absence of certain key microbes from our intestinal tract may set
us up for a variety of problems. This seems to be particularly true regarding the appropriate functioning of
the immune system. There are intriguing findings that suggest that the absence of these microbes is an
important contributor to the development of allergies and some autoimmune disorders. Research is currently
underway to test whether adding certain microbes to our internal ecosystem may help in the treatment of
these problems as well as in treating some forms of autism.
592 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 acidophile
alkaliphile
ammonification
anaerobic
anoxic
antibiotic
biofilm
biological nitrogen fixation
bioremediation
biotechnology
Black Death
botulism
CA-MRSA
capsule
chemotroph
conjugation
cyanobacteria
decomposer
denitrification
emerging disease
endemic disease
epidemic
extremophile
foodborne disease
Gram negative
Gram positive
halophile
hydrothermal vent
KEY TERMS
organism with optimal growth pH of three or below
organism with optimal growth pH of nine or above
process by which ammonia is released during the decomposition of nitrogen-containing organic
compounds
refers to organisms that grow without oxygen
without oxygen
biological substance that, in low concentration, is antagonistic to the growth of prokaryotes
microbial community that is held together by a gummy-textured matrix
conversion of atmospheric nitrogen into ammonia exclusively carried out by prokaryotes
use of microbial metabolism to remove pollutants
any technological application that uses living organisms, biological systems, or their derivatives to
produce or modify other products
devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium
Yersinia pestis
disease produce by the toxin of the anaerobic bacterium Clostridium botulinum
MRSA acquired in the community rather than in a hospital setting
external structure that enables a prokaryote to attach to surfaces and protects it from dehydration
organism that obtains energy from chemical compounds
process by which prokaryotes move DNA from one individual to another using a pilus
bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green
algae
organism that carries out the decomposition of dead organisms
transformation of nitrate from soil to gaseous nitrogen compounds such as N 2O, NO and N 2
disease making an initial appearance in a population or that is increasing in incidence or geographic
range
disease that is constantly present, usually at low incidence, in a population
disease that occurs in an unusually high number of individuals in a population at the same time
organism that grows under extreme or harsh conditions
any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria,
viruses, or other parasites that contaminate food
bacterium whose cell wall contains little peptidoglycan but has an outer membrane
bacterium that contains mainly peptidoglycan in its cell walls
organism that require a salt concentration of at least 0.2 M
fissure in Earth’s surface that releases geothermally heated water
Chapter 22 | Prokaryotes: Bacteria and Archaea 593 hyperthermophile
microbial mat
MRSA
nitrification
nitrogen fixation
nodule
nutrient
osmophile
pandemic
peptidoglycan
phototroph
pilus
pseudopeptidoglycan
psychrophile
radioresistant
resuscitation
S-layer
serotype
stromatolite
teichoic acid
thermophile
transduction
transformation
viable-but-non-culturable (VBNC) state
zoonosis
organism that grows at temperatures between 80–122 °C
multi-layered sheet of prokaryotes that may include bacteria and archaea
(methicillin-resistant Staphylococcus aureus ) very dangerous Staphylococcus aureus strain resistant to multiple
antibiotics
conversion of ammonium into nitrite and nitrate in soils
process by which gaseous nitrogen is transformed, or “fixed” into more readily available forms such as
ammonia
novel structure on the roots of certain plants (legumes) that results from the symbiotic interaction between the plant
and soil bacteria, is the site of nitrogen fixation
essential substances for growth, such as carbon and nitrogen
organism that grows in a high sugar concentration
widespread, usually worldwide, epidemic disease
material composed of polysaccharide chains cross-linked to unusual peptides
organism that is able to make its own food by converting solar energy to chemical energy
surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes
component of archaea cell walls that is similar to peptidoglycan in morphology but contains
different sugars
organism that grows at temperatures of -15 °C or lower
organism that grows in high levels of radiation
process by which prokaryotes that are in the VBNC state return to viability
surface-layer protein present on the outside of cell walls of archaea and bacteria
strain of bacteria that carries a set of similar antigens on its cell surface, often many in a bacterial species
layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats
polymer associated with the cell wall of Gram-positive bacteria
organism that lives at temperatures between 60–80 °C
process by which a bacteriophage moves DNA from one prokaryote to another
process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes
survival mechanism of bacteria facing environmental stress conditions
disease that primarily infects animals that is transmitted to humans
CHAPTER SUMMARY
22.1 Prokaryotic Diversity
Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may
have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth,
and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of
prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion
years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early
594 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of
other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures
formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.
Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called
extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in
the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response
to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A
biofilm is a microbial community held together in a gummy-textured matrix.
22.2 Structure of Prokaryotes
Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of
circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the
plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and
Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal
membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers
instead of bilayers.
The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls
varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but
they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided
into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms
have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope
containing lipopolysaccharides and lipoproteins.
22.3 Prokaryotic Metabolism
Prokaryotes are the most metabolically diverse organisms; they flourish in many different environments with various
carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large
amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements.
Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require
various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble
macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain
energy from chemical compounds.
Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of
animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release
carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial
decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions,
nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is
anaerobically catabolized by some prokaryotes, yielding N 2as the final product. Nitrification is the conversion of
ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and
transforms nitrate from soils into gaseous nitrogen compounds, such as N 2O, NO, and N 2.
22.4 Bacterial Diseases in Humans
Devastating diseases and plagues have been among us since early times. There are records about microbial diseases as far
back as 3000 B.C. Infectious diseases remain among the leading causes of death worldwide. Emerging diseases are those
rapidly increasing in incidence or geographic range. They can be new or re-emerging diseases (previously under control).
Many emerging diseases affecting humans, such as brucellosis, are zoonoses. The WHO has identified a group of diseases
whose re-emergence should be monitored: Those caused by bacteria include bubonic plague, diphtheria, and cholera.
Biofilms are considered responsible for diseases such as bacterial infections in patients with cystic fibrosis, Legionnaires’
disease, and otitis media. They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic
devices; and infect contact lenses, open wounds, and burned tissue. Biofilms also produce foodborne diseases because they
colonize the surfaces of food and food-processing equipment. Biofilms are resistant to most of the methods used to control
microbial growth. The excessive use of antibiotics has resulted in a major global problem, since resistant forms of bacteria
have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked
havoc recently. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or
parasites that contaminate food.
Chapter 22 | Prokaryotes: Bacteria and Archaea 595 22.5 Beneficial Prokaryotes
Pathogens are only a small percentage of all prokaryotes. In fact, our life would not be possible without prokaryotes.
Nitrogen is usually the most limiting element in terrestrial ecosystems; atmospheric nitrogen, the largest pool of available
nitrogen, is unavailable to eukaryotes. Nitrogen can be “fixed,” or converted into ammonia (NH 3) either biologically or
abiotically. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes. After photosynthesis, BNF is the
second most important biological process on Earth. The most important source of BNF is the symbiotic interaction
between soil bacteria and legume plants.
Microbial bioremediation is the use of microbial metabolism to remove pollutants. Bioremediation has been used to
remove agricultural chemicals that leach from soil into groundwater and the subsurface. Toxic metals and oxides, such as
selenium and arsenic compounds, can also be removed by bioremediation. Probably one of the most useful and interesting
examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills.
Human life is only possible due to the action of microbes, both those in the environment and those species that call us
home. Internally, they help us digest our food, produce crucial nutrients for us, protect us from pathogenic microbes, and
help train our immune systems to function correctly.
ART CONNECTION QUESTIONS
1. Figure 22.8 Compared to free-floating bacteria,
bacteria in biofilms often show increased resistance to
antibiotics and detergents. Why do you think this might be
the case?
2. Figure 22.15 Which of the following statements is true?
a. Gram-positive bacteria have a single cell wall
anchored to the cell membrane by lipoteichoic
acid.
b. Porins allow entry of substances into both Gram-
positive and Gram-negative bacteria.
c. The cell wall of Gram-negative bacteria is thick,
and the cell wall of Gram-positive bacteria is
thin.
d. Gram-negative bacteria have a cell wall made of
peptidoglycan, whereas Gram-positive bacteria
have a cell wall made of lipoteichoic acid.
3. Figure 22.19 Which of the following statements about
the nitrogen cycle is false?
a. Nitrogen fixing bacteria exist on the root
nodules of legumes and in the soil.
b. Denitrifying bacteria convert nitrates (NO 3-) into
nitrogen gas (N 2).
c. Ammonification is the process by which
ammonium ion (NH 4+) is released from
decomposing organic compounds.
d. Nitrification is the process by which nitrites
(NO 2-) are converted to ammonium ion (NH 4+).
REVIEW QUESTIONS
4. The first forms of life on Earth were thought to
be_________.
a. single-celled plants
b. prokaryotes
c. insects
d. large animals such as dinosaurs
5. Microbial mats __________.
a. are the earliest forms of life on Earth
b. obtained their energy and food from
hydrothermal vents
c. are multi-layered sheet of prokaryotes including
mostly bacteria but also archaea
d. all of the above
6. The first organisms that oxygenated the atmosphere
were
a. cyanobacteria
b. phototrophic organisms
c. anaerobic organisms
d. all of the above
7. Halophiles are organisms that require________.
a. a salt concentration of at least 0.2 M
b. high sugar concentration
c. the addition of halogens
d. all of the above
8. The presence of a membrane-enclosed nucleus is a
characteristic of ________.
a. prokaryotic cells
b. eukaryotic cells
c. all cells
d. viruses
9. Which of the following consist of prokaryotic cells?
a. bacteria and fungi
b. archaea and fungi
c. protists and animals
d. bacteria and archaea
10. The cell wall is ________.
a. interior to the cell membrane
596 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 b. exterior to the cell membrane
c. a part of the cell membrane
d. interior or exterior, depending on the particular
cell
11. Organisms most likely to be found in extreme
environments are ________.
a. fungi
b. bacteria
c. viruses
d. archaea
12. Prokaryotes stain as Gram-positive or Gram-negative
because of differences in the cell _______.
a. wall
b. cytoplasm
c. nucleus
d. chromosome
13. Pseudopeptidoglycan is a characteristic of the walls of
________.
a. eukaryotic cells
b. bacterial prokaryotic cells
c. archaean prokaryotic cells
d. bacterial and archaean prokaryotic cells
14. The lipopolysaccharide layer (LPS) is a characteristic
of the wall of ________.
a. archaean cells
b. Gram-negative bacteria
c. bacterial prokaryotic cells
d. eukaryotic cells
15. Which of the following elements is not a
micronutrient?
a. boron
b. calcium
c. chromium
d. manganese
16. Prokaryotes that obtain their energy from chemical
compounds are called _____.
a. phototrophs
b. auxotrophs
c. chemotrophs
d. lithotrophs
17. Ammonification is the process by which _____.
a. ammonia is released during the decomposition
of nitrogen-containing organic compounds
b. ammonium is converted to nitrite and nitrate in
soils
c. nitrate from soil is transformed to gaseous
nitrogen compounds such as NO, N 2O, and N 2
d. gaseous nitrogen is fixed to yield ammonia
18. Plants use carbon dioxide from the air and are
therefore called _____.
a. consumers
b. producers
c. decomposer
d. carbon fixers
19. A disease that is constantly present in a population is
called _____.
a. pandemic
b. epidemic
c. endemic
d. re-emerging
20. Which of the statements about biofilms is incorrect?
a. Biofilms are considered responsible for diseases
such as cystic fibrosis.
b. Biofilms produce dental plaque, and colonize
catheters and prostheses.
c. Biofilms colonize open wounds and burned
tissue.
d. All statements are incorrect.
21. Which of these statements is true?
a. An antibiotic is any substance produced by a
organism that is antagonistic to the growth of
prokaryotes.
b. An antibiotic is any substance produced by a
prokaryote that is antagonistic to the growth of
other viruses.
c. An antibiotic is any substance produced by a
prokaryote that is antagonistic to the growth of
eukaryotic cells.
d. An antibiotic is any substance produced by a
prokaryote that prevents growth of the same
prokaryote.
22. Which of these occurs through symbiotic nitrogen
fixation?
a. The plant benefits from using an endless source
of nitrogen.
b. The soil benefits from being naturally fertilized.
c. Bacteria benefit from using photosynthates from
the plant.
d. All of the above occur.
23. Synthetic compounds found in an organism but not
normally produced or expected to be present in that
organism are called _____.
a. pesticides
b. bioremediators
c. recalcitrant compounds
d. xenobiotics
24. Bioremediation includes _____.
a. the use of prokaryotes that can fix nitrogen
b. the use of prokaryotes to clean up pollutants
c. the use of prokaryotes as natural fertilizers
d. All of the above
CRITICAL THINKING QUESTIONS
Chapter 22 | Prokaryotes: Bacteria and Archaea 597 25. Describe briefly how you would detect the presence of
a non-culturable prokaryote in an environmental sample.
26. Why do scientists believe that the first organisms on
Earth were extremophiles?
27. Mention three differences between bacteria and
archaea.
28. Explain the statement that both types, bacteria and
archaea, have the same basic structures, but built from
different chemical components.
29. Think about the conditions (temperature, light,
pressure, and organic and inorganic materials) that you
may find in a deep-sea hydrothermal vent. What type of
prokaryotes, in terms of their metabolic needs (autotrophs,
phototrophs, chemotrophs, etc.), would you expect to find
there?
30. Explain the reason why the imprudent and excessive
use of antibiotics has resulted in a major global problem.
31. Researchers have discovered that washing spinach
with water several times does not prevent foodborne
diseases due to E. coli . How can you explain this fact?
32. Your friend believes that prokaryotes are always
detrimental and pathogenic. How would you explain to
them that they are wrong?
598 Chapter 22 | Prokaryotes: Bacteria and Archaea
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 23 | PROTISTS
Figure 23.1 Protists range from the microscopic, single-celled (a) Acanthocystis turfacea and the (b) ciliate
Tetrahymena thermophila , both visualized here using light microscopy, to the enormous, multicellular (c) kelps
(Chromalveolata) that extend for hundreds of feet in underwater “forests.” (credit a: modification of work by Yuiuji Tsukii;
credit b: modification of work by Richard Robinson, Public Library of Science; credit c: modification of work by Kip
Evans, NOAA; scale-bar data from Matt Russell)
Chapter Outline
23.1: Eukaryotic Origins
23.2: Characteristics of Protists
23.3: Groups of Protists
23.4: Ecology of Protists
Introduction
Humans have been familiar with macroscopic organisms (organisms big enough to see with the unaided eye) since before
there was a written history, and it is likely that most cultures distinguished between animals and land plants, and most
probably included the macroscopic fungi as plants. Therefore, it became an interesting challenge to deal with the world of
microorganisms once microscopes were developed a few centuries ago. Many different naming schemes were used over the
last couple of centuries, but it has become the most common practice to refer to eukaryotes that are not land plants, animals,
or fungi as protists.
This name was first suggested by Ernst Haeckel in the late nineteenth century. It has been applied in many contexts and
has been formally used to represent a kingdom-level taxon called Protista. However, many modern systematists (biologists
who study the relationships among organisms) are beginning to shy away from the idea of formal ranks such as kingdom
and phylum. Instead, they are naming taxa as groups of organisms thought to include all the descendants of a last common
ancestor (monophyletic group). During the past two decades, the field of molecular genetics has demonstrated that some
protists are more related to animals, plants, or fungi than they are to other protists. Therefore, not including animals,
plants and fungi make the kingdom Protista a paraphyletic group, or one that does not include all descendents of its
common ancestor. For this reason, protist lineages originally classified into the kingdom Protista continue to be examined
and debated. In the meantime, the term “protist” still is used informally to describe this tremendously diverse group of
eukaryotes.
Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine
environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants. Others invade
the cells of other protists, animals, and plants. Not all protists are microscopic. Some have huge, macroscopic cells, such as
the plasmodia (giant amoebae) of myxomycete slime molds or the marine green alga Caulerpa , which can have single cells
Chapter 23 | Protists 599 that can be several meters in size. Some protists are multicellular, such as the red, green, and brown seaweeds. It is among
the protists that one finds the wealth of ways that organisms can grow.
23.1 | Eukaryotic Origins
By the end of this section, you will be able to:
• List the unifying characteristics of eukaryotes
• Describe what scientists know about the origins of eukaryotes based on the last common ancestor
• Explain endosymbiotic theory
Living things fall into three large groups: Archaea, Bacteria, and Eukarya. The first two have prokaryotic cells, and the third
contains all eukaryotes. A relatively sparse fossil record is available to help discern what the first members of each of these
lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain
unknown. However, comparative biology of extant organisms and the limited fossil record provide some insight into the
history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria. They are about 3.5 billion years old and
are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other
prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Most living eukaryotes have
cells measuring 10 µm or greater. Structures this size, which might be fossils, appear in the geological record about 2.1
billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion that living eukaryotes are all descendants of a
single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following
characteristics must have been present in the last common ancestor, because these characteristics are present in at least some
of the members of each major lineage.
1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both
necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other
members of their lineages have “typical” mitochondria.
3. A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All
extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but they
are descended from ancestors that possessed them.
5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The
few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of
the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle
undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to
create a diploid zygote nucleus.
8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor
could make cell walls during some stage of its life cycle. However, not enough is known about eukaryotes’ cell walls
and their development to know how much homology exists among them. If the last common ancestor could make cell
walls, it is clear that this ability must have been lost in many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of
a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence”
inside it. This major theme in the origin of eukaryotes is known as endosymbiosis , one cell engulfing another such that the
600 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms
that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to
the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes
(Figure 23.5 ). Before explaining this further, it is necessary to consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of these, such as nitrogen fixation, are never found
in eukaryotes. The process of aerobic respiration is found in all major lineages of eukaryotes, and it is localized in the
mitochondria. Aerobic respiration is also found in many lineages of prokaryotes, but it is not present in all of them,
and many forms of evidence suggest that such anaerobic prokaryotes never carried out aerobic respiration nor did their
ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O 2), geological evidence shows that it originally lacked O 2.
Without oxygen, aerobic respiration would not be expected, and living things would have relied on fermentation instead.
At some point before, about 3.5 billion years ago, some prokaryotes began using energy from sunlight to power anabolic
processes that reduce carbon dioxide to form organic compounds. That is, they evolved the ability to photosynthesize.
Hydrogen, derived from various sources, was captured using light-powered reactions to reduce fixed carbon dioxide in the
Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and
released O 2as a waste product.
Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living
organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms
from oxygen, one of which, aerobic respiration, also generated high levels of ATP. It became widely present among
prokaryotes, including in a group we now call alpha-proteobacteria. Organisms that did not acquire aerobic respiration had
to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where
cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to
higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2 billion years old, so they appeared as oxygen
levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These
organelles were first observed by light microscopists in the late 1800s, where they appeared to be somewhat worm-shaped
structures that seemed to be moving around in the cell. Some early observers suggested that they might be bacteria living
inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that mitochondria were the organelles responsible
for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotic
theory , which states that eukaryotes may have been a product of one cell engulfing another, one living within another, and
evolving over time until the separate cells were no longer recognizable as such. In 1967, Margulis introduced new work
on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initially was met
with resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on
uncovering the steps involved in this evolutionary process and the key players involved. Much still remains to be discovered
about the origins of the cells that now make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and
expression appear closely related to those in Archaea. On the other hand, the metabolic organelles and genes responsible
for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship
occurred; this continues to be an exciting field of discovery in biology. For instance, it is not known whether the
endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be
among the extinct precursors of the last common ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Eukaryotic cells
may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption.
Each mitochondrion measures 1 to 10 or greater micrometers in length and exists in the cell as an organelle that can be
ovoid to worm-shaped to intricately branched ( Figure 23.2 ). Mitochondria arise from the division of existing mitochondria;
they may fuse together; and they may be moved around inside the cell by interactions with the cytoskeleton. However,
mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful
aerobic prokaryotes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed
a free-living aerobic prokaryote, specifically an alpha-proteobacterium, thereby giving the host cell the ability to use oxygen
to release energy stored in nutrients. Alpha-proteobacteria are a large group of bacteria that includes species symbiotic with
plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several
Chapter 23 | Protists 601 lines of evidence support that mitochondria are derived from this endosymbiotic event. Most mitochondria are shaped like
alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism
was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and
involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix
and inner membrane are rich with the enzymes necessary for aerobic respiration.
Figure 23.2 In this transmission electron micrograph of mitochondria in a mammalian lung cell, the cristae, infoldings
of the mitochondrial inner membrane, can be seen in cross-section. (credit: Louise Howard)
Mitochondria divide independently by a process that resembles binary fission in prokaryotes. Specifically, mitochondria are
not formed from scratch (de novo) by the eukaryotic cell; they reproduce within it and are distributed with the cytoplasm
when a cell divides or two cells fuse. Therefore, although these organelles are highly integrated into the eukaryotic cell,
they still reproduce as if they are independent organisms within the cell. However, their reproduction is synchronized with
the activity and division of the cell. Mitochondria have their own (usually) circular DNA chromosome that is stabilized by
attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also
have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support that
mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes, with genes similar to those in alpha-proteobacteria.
However, many of the genes for respiratory proteins are located in the nucleus. When these genes are compared to those of
other organisms, they appear to be of alpha-proteobacterial origin. Additionally, in some eukaryotic groups, such genes are
found in the mitochondria, whereas in other groups, they are found in the nucleus. This has been interpreted as evidence
that genes have been transferred from the endosymbiont chromosome to the host genome. This loss of genes by the
endosymbiont is probably one explanation why mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of too much oxygen. Some appear to lack
organelles that could be recognized as mitochondria. In the 1970s to the early 1990s, many biologists suggested that some of
these eukaryotes were descended from ancestors whose lineages had diverged from the lineage of mitochondrion-containing
eukaryotes before endosymbiosis occurred. However, later findings suggest that reduced organelles are found in most, if not
all, anaerobic eukaryotes, and that all eukaryotes appear to carry some genes in their nuclei that are of mitochondrial origin.
In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions
is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated
with the reduced mitochondrion-derived organelles of anaerobic eukaryotes. Therefore, most biologists accept that the last
common ancestor of eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in addition to the standard eukaryotic organelles, another
kind of organelle called a plastid . When such cells are carrying out photosynthesis, their plastids are rich in the pigment
chlorophyll aand a range of other pigments, called accessory pigments, which are involved in harvesting energy from light.
Photosynthetic plastids are called chloroplasts ( Figure 23.3 ).
602 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 23.3 (a) This chloroplast cross-section illustrates its elaborate inner membrane organization. Stacks of
thylakoid membranes compartmentalize photosynthetic enzymes and provide scaffolding for chloroplast DNA. (b) In
this micrograph of Elodea sp., the chloroplasts can be seen as small green spheres. (credit b: modification of work by
Brandon Zierer; scale-bar data from Matt Russell)
Like mitochondria, plastids appear to have an endosymbiotic origin. This hypothesis was also championed by Lynn
Margulis. Plastids are derived from cyanobacteria that lived inside the cells of an ancestral, aerobic, heterotrophic eukaryote.
This is called primary endosymbiosis, and plastids of primary origin are surrounded by two membranes. The best evidence
is that this has happened twice in the history of eukaryotes. In one case, the common ancestor of the major lineage/
supergroup Archaeplastida took on a cyanobacterial endosymbiont; in the other, the ancestor of the small amoeboid
rhizarian taxon, Paulinella , took on a different cyanobacterial endosymbiont. Almost all photosynthetic eukaryotes are
descended from the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the conventional structures of the group. However, unlike
most prokaryotes, they have extensive, internal membrane-bound sacs called thylakoids. Chlorophyll is a component
of these membranes, as are many of the proteins of the light reactions of photosynthesis. Cyanobacteria also have the
peptidoglycan wall and lipopolysaccharide layer associated with Gram-negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA chromosome, and ribosomes similar to those of
cyanobacteria. Each chloroplast is surrounded by two membranes. In the group of Archaeplastida called the glaucophytes
and in Paulinella , a thin peptidoglycan layer is present between the outer and inner plastid membranes. All other plastids
lack this relictual cyanobacterial wall. The outer membrane surrounding the plastid is thought to be derived from the vacuole
in the host, and the inner membrane is thought to be derived from the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many of the genes of the endosymbiont were transferred
to the nucleus. Plastids, like mitochondria, cannot live independently outside the host. In addition, like mitochondria,
plastids are derived from the division of other plastids and never built from scratch. Researchers have suggested that the
endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion years ago, at least 5 hundred million years after the
fossil record suggests that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary endosymbiosis. Some of the major groups of algae became
photosynthetic by secondary endosymbiosis, that is, by taking in either green algae or red algae (both from Archaeplastida)
as endosymbionts ( Figure 23.4 ab ). Numerous microscopic and genetic studies have supported this conclusion. Secondary
plastids are surrounded by three or more membranes, and some secondary plastids even have clear remnants of the nucleus
of endosymbiotic alga. Others have not “kept” any remnants. There are cases where tertiary or higher-order endosymbiotic
events are the best explanations for plastids in some eukaryotes.
Chapter 23 | Protists 603 Figure 23.4 (a) Red algae and (b) green algae (visualized by light microscopy) share similar DNA sequences with
photosynthetic cyanobacteria. Scientists speculate that, in a process called endosymbiosis, an ancestral prokaryote
engulfed a photosynthetic cyanobacterium that evolved into modern-day chloroplasts. (credit a: modification of work
by Ed Bierman; credit b: modification of work by G. Fahnenstiel, NOAA; scale-bar data from Matt Russell)
Figure 23.5 The first eukaryote may have originated from an ancestral prokaryote that had undergone membrane
proliferation, compartmentalization of cellular function (into a nucleus, lysosomes, and an endoplasmic reticulum),
and the establishment of endosymbiotic relationships with an aerobic prokaryote, and, in some cases, a
photosynthetic prokaryote, to form mitochondria and chloroplasts, respectively.
What evidence is there that mitochondria were incorporated into the ancestral eukaryotic cell before
chloroplasts?
604 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a coevolved relationship in which
neither cell could survive alone. The chloroplasts of red and green algae, for instance, are derived from the
engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an endosymbiont to itself become engulfed,
resulting in a secondary endosymbiosis. Molecular and morphological evidence suggest that the
chlorarachniophyte protists are derived from a secondary endosymbiotic event. Chlorarachniophytes are
rare algae indigenous to tropical seas and sand that can be classified into the rhizarian supergroup.
Chlorarachniophytes extend thin cytoplasmic strands, interconnecting themselves with other
chlorarachniophytes, in a cytoplasmic network. These protists are thought to have originated when a
eukaryote engulfed a green alga, the latter of which had already established an endosymbiotic relationship
with a photosynthetic cyanobacterium ( Figure 23.6 ).
Figure 23.6 The hypothesized process of endosymbiotic events leading to the evolution of chlorarachniophytes is
shown. In a primary endosymbiotic event, a heterotrophic eukaryote consumed a cyanobacterium. In a secondary
endosymbiotic event, the cell resulting from primary endosymbiosis was consumed by a second cell. The resulting
organelle became a plastid in modern chlorarachniophytes.
Several lines of evidence support that chlorarachniophytes evolved from secondary endosymbiosis. The
chloroplasts contained within the green algal endosymbionts still are capable of photosynthesis, making
chlorarachniophytes photosynthetic. The green algal endosymbiont also exhibits a stunted vestigial nucleus.
In fact, it appears that chlorarachniophytes are the products of an evolutionarily recent secondary
endosymbiotic event. The plastids of chlorarachniophytes are surrounded by four membranes: The first two
correspond to the inner and outer membranes of the photosynthetic cyanobacterium, the third corresponds
to the green alga, and the fourth corresponds to the vacuole that surrounded the green alga when it was
engulfed by the chlorarachniophyte ancestor. In other lineages that involved secondary endosymbiosis, only
three membranes can be identified around plastids. This is currently rectified as a sequential loss of a
membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to chlorarachniophytes. In fact, secondary
endosymbiosis of green algae also led to euglenid protists, whereas secondary endosymbiosis of red algae
led to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
23.2 | Characteristics of Protists
By the end of this section, you will be able to:
• Describe the cell structure characteristics of protists
• Describe the metabolic diversity of protists
• Describe the life cycle diversity of protists
Chapter 23 | Protists 605 There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since
many protists live as commensals or parasites in other organisms and these relationships are often species-specific, there is
a huge potential for protist diversity that matches the diversity of hosts. As the catchall term for eukaryotic organisms that
are not animal, plant, or fungi, it is not surprising that very few characteristics are common to all protists.
Cell Structure
The cells of protists are among the most elaborate of all cells. Most protists are microscopic and unicellular, but some true
multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living cells and in
other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look
like amorphous blobs of slime, or in other cases, like ferns. In fact, many protist cells are multinucleated; in some species,
the nuclei are different sizes and have distinct roles in protist cell function.
Single protist cells range in size from less than a micrometer to three meters in length to hectares. Protist cells may be
enveloped by animal-like cell membranes or plant-like cell walls. Others are encased in glassy silica-based shells or wound
with pellicles of interlocking protein strips. The pellicle functions like a flexible coat of armor, preventing the protist from
being torn or pierced without compromising its range of motion.
Metabolism
Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Protists that store energy by photosynthesis belong
to a group of photoautotrophs and are characterized by the presence of chloroplasts. Other protists are heterotrophic and
consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist
species ingest particles by a process called phagocytosis, in which the cell membrane engulfs a food particle and brings
it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole ( Figure 23.7 ). The vesicle
containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a
phagolysosome , and the food particle is broken down into small molecules that can diffuse into the cytoplasm and be used
in cellular metabolism. Undigested remains ultimately are expelled from the cell via exocytosis.
Figure 23.7 The stages of phagocytosis include the engulfment of a food particle, the digestion of the particle using
hydrolytic enzymes contained within a lysosome, and the expulsion of undigested materials from the cell.
Subtypes of heterotrophs, called saprobes, absorb nutrients from dead organisms or their organic wastes. Some protists can
function as mixotrophs , obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or
organic nutrients are available.
Motility
The majority of protists are motile, but different types of protists have evolved varied modes of movement ( Figure 23.8 ).
Some protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that
they coordinately beat to swim. Still others form cytoplasmic extensions called pseudopodia anywhere on the cell, anchor
the pseudopodia to a substrate, and pull themselves forward. Some protists can move toward or away from a stimulus, a
movement referred to as taxis. Movement toward light, termed phototaxis, is accomplished by coupling their locomotion
strategy with a light-sensing organ.
606 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 23.8 Protists use various methods for transportation. (a) Paramecium waves hair-like appendages called cilia
to propel itself. (b) Amoeba uses lobe-like pseudopodia to anchor itself to a solid surface and pull itself forward. (c)
Euglena uses a whip-like tail called a flagellum to propel itself.
Life Cycles
Protists reproduce by a variety of mechanisms. Most undergo some form of asexual reproduction, such as binary fission, to
produce two daughter cells. In protists, binary fission can be divided into transverse or longitudinal, depending on the axis
of orientation; sometimes Paramecium exhibits this method. Some protists such as the true slime molds exhibit multiple
fission and simultaneously divide into many daughter cells. Others produce tiny buds that go on to divide and grow to the
size of the parental protist. Sexual reproduction, involving meiosis and fertilization, is common among protists, and many
protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction is often associated
with periods when nutrients are depleted or environmental changes occur. Sexual reproduction may allow the protist to
recombine genes and produce new variations of progeny that may be better suited to surviving in the new environment.
However, sexual reproduction is often associated with resistant cysts that are a protective, resting stage. Depending on their
habitat, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows
certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried
(such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no
cellular metabolism.
Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must
infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in
the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular
stages in both haploid and diploid forms, a strategy called alternation of generations that is also used by plants.
Habitats
Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and
even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms
or their wastes, and contribute to their decay.
23.3 | Groups of Protists
By the end of this section, you will be able to:
• Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
• Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups
of eukaryotes
In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed
new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar
morphological features may have evolved analogous structures because of similar selective pressures—rather than because
of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so
challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all
of the protists as well as animals, plants, and fungi that evolved from a common ancestor ( Figure 23.9 ). The supergroups
Chapter 23 | Protists 607 are believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a
single common ancestor, and thus all members are most closely related to each other than to organisms outside that group.
There is still evidence lacking for the monophyly of some groups.
Figure 23.9 This diagram shows a proposed classification of the domain Eukara. Currently, the domain Eukarya
is divided into six supergroups. Within each supergroup are multiple kingdoms. Dotted lines indicate suggested
evolutionary relationships that remain under debate.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a more appropriate
hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that the classification scheme presented
here is just one of several hypotheses, and the true evolutionary relationships are still to be determined. When learning about
protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that define the groups
themselves.
608 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Excavata
Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding
groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites.
Its subgroups are the diplomonads, parabasalids, and euglenozoans.
Diplomonads
Among the Excavata are the diplomonads, which include the intestinal parasite, Giardia lamblia (Figure 23.10 ). Until
recently, these protists were believed to lack mitochondria. Mitochondrial remnant organelles, called mitosomes , have
since been identified in diplomonads, but these mitosomes are essentially nonfunctional. Diplomonads exist in anaerobic
environments and use alternative pathways, such as glycolysis, to generate energy. Each diplomonad cell has two identical
nuclei and uses several flagella for locomotion.
Figure 23.10 The mammalian intestinal parasite Giardia lamblia , visualized here using scanning electron microscopy,
is a waterborne protist that causes severe diarrhea when ingested. (credit: modification of work by Janice Carr, CDC;
scale-bar data from Matt Russell)
Parabasalids
A second Excavata subgroup, the parabasalids, also exhibits semi-functional mitochondria. In parabasalids, these structures
function anaerobically and are called hydrogenosomes because they produce hydrogen gas as a byproduct. Parabasalids
move with flagella and membrane rippling. Trichomonas vaginalis , a parabasalid that causes a sexually transmitted
disease in humans, employs these mechanisms to transit through the male and female urogenital tracts. T.vaginalis
causes trichamoniasis, which appears in an estimated 180 million cases worldwide each year. Whereas men rarely exhibit
symptoms during an infection with this protist, infected women may become more susceptible to secondary infection with
human immunodeficiency virus (HIV) and may be more likely to develop cervical cancer. Pregnant women infected with
T.vaginalis are at an increased risk of serious complications, such as pre-term delivery.
Euglenozoans
Euglenozoans includes parasites, heterotrophs, autotrophs, and mixotrophs, ranging in size from 10 to 500 µm. Euglenoids
move through their aquatic habitats using two long flagella that guide them toward light sources sensed by a primitive ocular
organ called an eyespot. The familiar genus, Euglena , encompasses some mixotrophic species that display a photosynthetic
capability only when light is present. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning,
and the cells instead take up organic nutrients from their environment.
The human parasite, Trypanosoma brucei , belongs to a different subgroup of Euglenozoa, the kinetoplastids. The
kinetoplastid subgroup is named after the kinetoplast , a DNA mass carried within the single, oversized mitochondrion
possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause
devastating human diseases and infect an insect species during a portion of their life cycle. T.brucei develops in the gut of
the tsetse fly after the fly bites an infected human or other mammalian host. The parasite then travels to the insect salivary
glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. T.
Chapter 23 | Protists 609 brucei is common in central Africa and is the causative agent of African sleeping sickness, a disease associated with severe
chronic fatigue, coma, and can be fatal if left untreated.
Figure 23.11 Trypanosoma brucei , the causative agent of sleeping sickness, spends part of its life cycle in the tsetse
fly and part in humans. (credit: modification of work by CDC)
Wa t c h this video (http://openstaxcollege.org/l/T_brucei) to see T.brucei swimming.
Chromalveolata
Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed
a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with
a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary
endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid
genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to
change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant
disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.
Alveolates: Dinoflagellates, Apicomplexians, and Ciliates
A large body of data supports that the alveolates are derived from a shared common ancestor. The alveolates are named for
the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is
unknown, but it may be involved in osmoregulation. The alveolates are further categorized into some of the better-known
protists: the dinoflagellates, the apicomplexans, and the ciliates.
Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many
dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the
cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate ( Figure 23.12 ).
Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater
610 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 and marine habitats, and are a component of plankton , the typically microscopic organisms that drift through the water and
serve as a crucial food source for larger aquatic organisms.
Figure 23.12 The dinoflagellates exhibit great diversity in shape. Many are encased in cellulose armor and have two
flagella that fit in grooves between the plates. Movement of these two perpendicular flagella causes a spinning motion.
Some dinoflagellates generate light, called bioluminescence , when they are jarred or stressed. Large numbers of marine
dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on
a brilliant blue color ( Figure 23.13 ). For approximately 20 species of marine dinoflagellates, population explosions (also
called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red
tide, and it results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate
species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental
to commercial fisheries, and humans who consume these protists may become poisoned.
Figure 23.13 Bioluminescence is emitted from dinoflagellates in a breaking wave, as seen from the New Jersey coast.
(credit: “catalano82”/Flickr)
The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed
at one end of the cell in a structure called an apical complex ( Figure 23.14 ). The apical complex is specialized for entry
and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium , which
causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual
reproduction.
Chapter 23 | Protists 611 Figure 23.14 (a) Apicomplexans are parasitic protists. They have a characteristic apical complex that enables them to
infect host cells. (b) Plasmodium , the causative agent of malaria, has a complex life cycle typical of apicomplexans.
(credit b: modification of work by CDC)
The ciliates, which include Paramecium and Tetrahymena , are a group of protists 10 to 3,000 micrometers in length that
are covered in rows, tufts, or spirals of tiny cilia. By beating their cilia synchronously or in waves, ciliates can coordinate
directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles,
funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus
Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which
is used to capture and digest bacteria ( Figure 23.15 ). Food captured in the oral groove enters a food vacuole, where it
combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the
cell membrane, called the anal pore. In addition to a vacuole-based digestive system, Paramecium also uses contractile
vacuoles , which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze
water from the cell.
Figure 23.15 Paramecium has a primitive mouth (called an oral groove) to ingest food, and an anal pore to excrete
it. Contractile vacuoles allow the organism to excrete excess water. Cilia enable the organism to move. (credit
“paramecium micrograph”: modification of work by NIH; scale-bar data from Matt Russell)
Watch the video (http://openstaxcollege.org/l/paramecium) of the contractile vacuole of Paramecium expelling water
to keep the cell osmotically balanced.
612 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual
reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of
sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most
other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make
physical contact and join with a cytoplasmic bridge ( Figure 23.16 ). The diploid micronucleus in each cell then undergoes
meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then
undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move
away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates
a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of
mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become
full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new
macronuclei. Two cell divisions then yield four new Paramecia from each original conjugative cell.
Chapter 23 | Protists 613 Figure 23.16 The complex process of sexual reproduction in Paramecium creates eight daughter cells from two
original cells. Each cell has a macronucleus and a micronucleus. During sexual reproduction, the macronucleus
dissolves and is replaced by a micronucleus. (credit “micrograph”: modification of work by Ian Sutton; scale-bar
data from Matt Russell)
Which of the following statements about Paramecium sexual reproduction is false?
a. The macronuclei are derived from micronuclei.
b. Both mitosis and meiosis occur during sexual reproduction.
c. The conjugate pair swaps macronucleii.
d. Each parent produces four daughter cells.
Stramenopiles: Diatoms, Brown Algae, Golden Algae and Oomycetes
The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists.
The unifying feature of this group is the presence of a textured, or “hairy,” flagellum. Many stramenopiles also have an
614 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 additional flagellum that lacks hair-like projections ( Figure 23.17 ). Members of this subgroup range in size from single-
celled diatoms to the massive and multicellular kelp.
Figure 23.17 This stramenopile cell has a single hairy flagellum and a secondary smooth flagellum.
The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls
composed of silicon dioxide in a matrix of organic particles ( Figure 23.18 ). These protists are a component of freshwater
and marine plankton. Most species of diatoms reproduce asexually, although some instances of sexual reproduction
and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe . By expelling a stream of
mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction.
Figure 23.18 Assorted diatoms, visualized here using light microscopy, live among annual sea ice in McMurdo Sound,
Antarctica. Diatoms range in size from 2 to 200 µm. (credit: Prof. Gordon T. Taylor, Stony Brook University, NSF, NOAA)
During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic
organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on
dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during
photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean
is described as the biological carbon pump , because carbon is “pumped” to the ocean depths where it is inaccessible to the
atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower
atmospheric carbon dioxide levels.
Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold
color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange
Chapter 23 | Protists 615 in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton
community.
The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are
a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like
holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous,
extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of
generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans,
for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote
that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm
and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In
the brown algae genus Laminaria , haploid spores develop into multicellular gametophytes, which produce haploid gametes
that combine to produce diploid organisms that then become multicellular organisms with a different structure from the
haploid form ( Figure 23.19 ). Certain other organisms perform alternation of generations in which both the haploid and
diploid forms look the same.
Figure 23.19 Several species of brown algae, such as the Laminaria shown here, have evolved life cycles
in which both the haploid (gametophyte) and diploid (sporophyte) forms are multicellular. The gametophyte is
different in structure than the sporophyte. (credit “laminaria photograph”: modification of work by Claire Fackler,
CINMS, NOAA Photo Library)
Which of the following statements about the Laminaria life cycle is false?
a. 1 nzoospores form in the sporangia.
b. The sporophyte is the 2 nplant.
c. The gametophyte is diploid.
d. Both the gametophyte and sporophyte stages are multicellular.
The water molds, oomycetes (“egg fungus”), were so-named based on their fungus-like morphology, but molecular data
have shown that the water molds are not closely related to fungi. The oomycetes are characterized by a cellulose-based
cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have
two oppositely directed flagella (one hairy and one smooth) for locomotion. The oomycetes are nonphotosynthetic and
include many saprobes and parasites. The saprobes appear as white fluffy growths on dead organisms ( Figure 23.20 ). Most
oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans , the causative
agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.
616 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 23.20 A saprobic oomycete engulfs a dead insect. (credit: modification of work by Thomas Bresson)
Rhizaria
The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia
(Figure 23.21 ). Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These
pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its
cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming , is used
by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen.
Figure 23.21 Ammonia tepida , a Rhizaria species viewed here using phase contrast light microscopy, exhibits many
threadlike pseudopodia. (credit: modification of work by Scott Fay, UC Berkeley; scale-bar data from Matt Russell)
Take a look at this video (http://openstaxcollege.org/l/chara_corallina) to see cytoplasmic streaming in a green alga.
Forams
Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several
centimeters in length, and occasionally resembling tiny snails ( Figure 23.22 ). As a group, the forams exhibit porous shells,
called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may
Chapter 23 | Protists 617 house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and
allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other
particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global
weather patterns.
Figure 23.22 These shells from foraminifera sank to the sea floor. (credit: Deep East 2001, NOAA/OER)
Radiolarians
A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry
(Figure 23.23 ). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists
and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in
100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.
Figure 23.23 This fossilized radiolarian shell was imaged using a scanning electron microscope. (credit: modification
of work by Hannes Grobe, Alfred Wegener Institute; scale-bar data from Matt Russell)
Archaeplastida
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor of these protists
that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all
Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The
red and green algae include unicellular, multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists
to large, multicellular forms grouped into the informal seaweed category. The red algae life cycle is an alternation of
generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and
618 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 outcompete the green tint of chlorophyll, making these species appear as varying shades of red. Other protists classified as
red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at
depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly
in terms of chloroplast structure. That this group of protists shared a relatively recent common ancestor with land plants is
well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest
living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in
wet habitats, and their presence often signals a healthy ecosystem.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and
are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology
and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte
species exhibit haploid gametes and spores that resemble Chlamydomonas .
The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection
of individual cells, but in other ways like the specialized cells of a multicellular organism ( Figure 23.24 ).Volvox colonies
contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous
glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic
bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this
organism.
Figure 23.24 Volvox aureus is a green alga in the supergroup Archaeplastida. This species exists as a colony,
consisting of cells immersed in a gel-like matrix and intertwined with each other via hair-like cytoplasmic extensions.
(credit: Dr. Ralf Wagner)
True multicellular organisms, such as the sea lettuce, Ulva , are represented among the chlorophytes. In addition, some
chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and
can reach lengths of 3 meters ( Figure 23.25 ).Caulerpa species undergo nuclear division, but their cells do not complete
cytokinesis, remaining instead as massive and elaborate single cells.
Figure 23.25 Caulerpa taxifolia is a chlorophyte consisting of a single cell containing potentially thousands of nuclei.
(credit: NOAA)
Chapter 23 | Protists 619 Amoebozoa
The amoebozoans characteristically exhibit pseudopodia that extend like tubes or flat lobes, rather than the hair-like
pseudopodia of rhizarian amoeba ( Figure 23.26 ). The Amoebozoa include several groups of unicellular amoeba-like
organisms that are free-living or parasites.
Figure 23.26 Amoebae with tubular and lobe-shaped pseudopodia are seen under a microscope. These isolates would
be morphologically classified as amoebozoans.
Slime Molds
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the
result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting
bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds
are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding
stage ( Figure 23.27 ). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the
plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress.
Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to
potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid
cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
620 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 23.27 The life cycle of the plasmodial slime mold is shown. The brightly colored plasmodium in the inset photo is
a single-celled, multinucleate mass. (credit: modification of work by Dr. Jonatha Gott and the Center for RNA Molecular
Biology, Case Western Reserve University)
The cellular slime molds function as independent amoeboid cells when nutrients are abundant ( Figure 23.28 ). When food
is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some
cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual
fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate
if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium , which commonly
exists in the damp soil of forests.
Chapter 23 | Protists 621 Figure 23.28 Cellular slime molds may exist as solitary or aggregated amoebas. (credit: modification of work by
“thatredhead4”/Flickr)
View this site (http://openstaxcollege.org/l/slime_mold) to see the formation of a fruiting body by a cellular slime mold.
Opisthokonta
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of
sponges and, in fact, all animals. Choanoflagellates include unicellular and colonial forms, and number about 244 described
species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli.
The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of
choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship
to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans.
Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related
to animals. In the past, they were grouped with fungi and other protists based on their morphology.
622 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 23.4 | Ecology of Protists
By the end of this section, you will be able to:
• Describe the role that protists play in the ecosystem
• Describe important pathogenic species of protists
Protists function in various ecological niches. Whereas some protist species are essential components of the food chain and
generators of biomass, others function in the decomposition of organic materials. Still other protists are dangerous human
pathogens or causative agents of devastating plant diseases.
Primary Producers/Food Sources
Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are consumed
directly. Alternatively, photosynthetic protists serve as producers of nutrition for other organisms. For instance,
photosynthetic dinoflagellates called zooxanthellae use sunlight to fix inorganic carbon. In this symbiotic relationship, these
protists provide nutrients for coral polyps ( Figure 23.29 ) that house them, giving corals a boost of energy to secrete a
calcium carbonate skeleton. In turn, the corals provide the protist with a protected environment and the compounds needed
for photosynthesis. This type of symbiotic relationship is important in nutrient-poor environments. Without dinoflagellate
symbionts, corals lose algal pigments in a process called coral bleaching, and they eventually die. This explains why reef-
building corals do not reside in waters deeper than 20 meters: insufficient light reaches those depths for dinoflagellates to
photosynthesize.
Figure 23.29 Coral polyps obtain nutrition through a symbiotic relationship with dinoflagellates.
The protists themselves and their products of photosynthesis are essential—directly or indirectly—to the survival of
organisms ranging from bacteria to mammals ( Figure 23.30 ). As primary producers, protists feed a large proportion of the
world’s aquatic species. (On land, terrestrial plants serve as primary producers.) In fact, approximately one-quarter of the
world’s photosynthesis is conducted by protists, particularly dinoflagellates, diatoms, and multicellular algae.
Chapter 23 | Protists 623 Figure 23.30 Virtually all aquatic organisms depend directly or indirectly on protists for food. (credit “mollusks”:
modification of work by Craig Stihler, USFWS; credit “crab”: modification of work by David Berkowitz; credit “dolphin”:
modification of work by Mike Baird; credit “fish”: modification of work by Tim Sheerman-Chase; credit “penguin”:
modification of work by Aaron Logan)
Protists do not create food sources only for sea-dwelling organisms. For instance, certain anaerobic parabasalid species exist
in the digestive tracts of termites and wood-eating cockroaches, where they contribute an essential step in the digestion of
cellulose ingested by these insects as they bore through wood.
Human Pathogens
A pathogen is anything that causes disease. Parasites live in or on an organism and harm the organism. A significant number
of protists are pathogenic parasites that must infect other organisms to survive and propagate. Protist parasites include the
causative agents of malaria, African sleeping sickness, and waterborne gastroenteritis in humans. Other protist pathogens
prey on plants, effecting massive destruction of food crops.
Plasmodium Species
Members of the genus Plasmodium must colonize both a mosquito and a vertebrate to complete their life cycle. In
vertebrates, the parasite develops in liver cells and goes on to infect red blood cells, bursting from and destroying the
blood cells with each asexual replication cycle ( Figure 23.31 ). Of the four Plasmodium species known to infect humans,
P.falciparum accounts for 50 percent of all malaria cases and is the primary cause of disease-related fatalities in tropical
regions of the world. In 2010, it was estimated that malaria caused between one-half and one million deaths, mostly in
African children. During the course of malaria, P.falciparum can infect and destroy more than one-half of a human’s
624 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 circulating blood cells, leading to severe anemia. In response to waste products released as the parasites burst from infected
blood cells, the host immune system mounts a massive inflammatory response with episodes of delirium-inducing fever
as parasites lyse red blood cells, spilling parasite waste into the bloodstream. P.falciparum is transmitted to humans by
the African malaria mosquito, Anopheles gambiae . Techniques to kill, sterilize, or avoid exposure to this highly aggressive
mosquito species are crucial to malaria control.
Figure 23.31 Red blood cells are shown to be infected with P.falciparum , the causative agent of malaria. In this
light microscopic image taken using a 100× oil immersion lens, the ring-shaped P.falciparum stains purple. (credit:
modification of work by Michael Zahniser; scale-bar data from Matt Russell)
This movie (http://openstaxcollege.org/l/malaria) depicts the pathogenesis of Plasmodium falciparum , the causative
agent of malaria.
Trypanosomes
Trypanosoma brucei , the parasite that is responsible for African sleeping sickness, confounds the human immune system by
changing its thick layer of surface glycoproteins with each infectious cycle ( Figure 23.32 ). The glycoproteins are identified
by the immune system as foreign antigens, and a specific antibody defense is mounted against the parasite. However, T.
brucei has thousands of possible antigens, and with each subsequent generation, the protist switches to a glycoprotein
coating with a different molecular structure. In this way, T.brucei is capable of replicating continuously without the immune
system ever succeeding in clearing the parasite. Without treatment, T.brucei attacks red blood cells, causing the patient to
lapse into a coma and eventually die. During epidemic periods, mortality from the disease can be high. Greater surveillance
and control measures lead to a reduction in reported cases; some of the lowest numbers reported in 50 years (fewer than
10,000 cases in all of sub-Saharan Africa) have happened since 2009.
Chapter 23 | Protists 625 This movie (http://openstaxcollege.org/l/African_sleep) discusses the pathogenesis of Trypanosoma brucei , the
causative agent of African sleeping sickness.
In Latin America, another species, T.cruzi , is responsible for Chagas disease. T.cruzi infections are mainly caused by a
blood-sucking bug. The parasite inhabits heart and digestive system tissues in the chronic phase of infection, leading to
malnutrition and heart failure due to abnormal heart rhythms. An estimated 10 million people are infected with Chagas
disease, and it caused 10,000 deaths in 2008.
Figure 23.32 Trypanosomes are shown among red blood cells. (credit: modification of work by Dr. Myron G. Shultz;
scale-bar data from Matt Russell)
Plant Parasites
Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete Plasmopara viticola parasitizes
grape plants, causing a disease called downy mildew ( Figure 23.33 ). Grape plants infected with P.viticola appear stunted
and have discolored, withered leaves. The spread of downy mildew nearly collapsed the French wine industry in the
nineteenth century.
Figure 23.33 Both downy and powdery mildews on this grape leaf are caused by an infection of P.viticola . (credit:
modification of work by USDA)
Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks and stems to decay
into black slime ( Figure 23.34 ). Widespread potato blight caused by P.infestans precipitated the well-known Irish potato
626 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 famine in the nineteenth century that claimed the lives of approximately 1 million people and led to the emigration of at
least 1 million more from Ireland. Late blight continues to plague potato crops in certain parts of the United States and
Russia, wiping out as much as 70 percent of crops when no pesticides are applied.
Figure 23.34 These unappetizing remnants result from an infection with P.infestans , the causative agent of potato
late blight. (credit: USDA)
Agents of Decomposition
The fungus-like protist saprobes are specialized to absorb nutrients from nonliving organic matter, such as dead organisms
or their wastes. For instance, many types of oomycetes grow on dead animals or algae. Saprobic protists have the essential
function of returning inorganic nutrients to the soil and water. This process allows for new plant growth, which in turn
generates sustenance for other organisms along the food chain. Indeed, without saprobe species, such as protists, fungi, and
bacteria, life would cease to exist as all organic carbon became “tied up” in dead organisms.
Chapter 23 | Protists 627 biological carbon pump
bioluminescence
contractile vacuole
cytoplasmic streaming
endosymbiosis
endosymbiotic theory
hydrogenosome
kinetoplast
mitosome
mixotroph
pellicle
phagolysosome
plankton
plastid
raphe
test
KEY TERMS
process by which inorganic carbon is fixed by photosynthetic species that then die and fall to
the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the
atmosphere
generation and emission of light by an organism, as in dinoflagellates
vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water
from the cell; an osmoregulatory vesicle
movement of cytoplasm into an extended pseudopod such that the entire cell is transported to
the site of the pseudopod
engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the
process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
theory that states that eukaryotes may have been a product of one cell engulfing another, one
living within another, and evolving over time until the separate cells were no longer recognizable as such
organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a
byproduct; likely evolved from mitochondria
mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum:
Euglenozoa)
nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a
mitochondrion
organism that can obtain nutrition by autotrophic or heterotrophic means, usually facultatively
outer cell covering composed of interlocking protein strips that function like a flexible coat of armor, preventing
cells from being torn or pierced without compromising their range of motion
cellular body formed by the union of a phagosome containing the ingested particle with a lysosome that
contains hydrolytic enzymes
diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food
source for larger aquatic organisms
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and
pigments
slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion
and attachment to substrates
porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate
CHAPTER SUMMARY
23.1 Eukaryotic Origins
The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It
is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common
ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained
linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the
ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the
result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the
initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle,
but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life
cycles, and number of cells per individual.
628 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 23.2 Characteristics of Protists
Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an
artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of
reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are
motile, but these organisms use diverse structures for transportation.
23.3 Groups of Protists
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified
many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into
six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this
classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the
monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation
exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
23.4 Ecology of Protists
Protists function at several levels of the ecological food web: as primary producers, as direct food sources, and as
decomposers. In addition, many protists are parasites of plants and animals that can cause deadly human diseases or
destroy valuable crops.
ART CONNECTION QUESTIONS
1. Figure 23.5 What evidence is there that mitochondria
were incorporated into the ancestral eukaryotic cell before
chloroplasts?
2. Figure 23.15 Which of the following statements about
Paramecium sexual reproduction is false?
a. The macronuclei are derived from micronuclei.
b. Both mitosis and meiosis occur during sexual
reproduction.
c. The conjugate pair swaps macronuclei.
d. Each parent produces four daughter cells.
3. Figure 23.18 Which of the following statements about
the Laminaria life cycle is false?
a. 1nzoospores form in the sporangia.
b. The sporophyte is the 2n plant.
c. The gametophyte is diploid.
d. Both the gametophyte and sporophyte stages are
multicellular.
REVIEW QUESTIONS
4. What event is thought to have contributed to the
evolution of eukaryotes?
a. global warming
b. glaciation
c. volcanic activity
d. oxygenation of the atmosphere
5. Which characteristic is shared by prokaryotes and
eukaryotes?
a. cytoskeleton
b. nuclear envelope
c. DNA-based genome
d. mitochondria
6. Mitochondria most likely evolved by _____________.
a. a photosynthetic cyanobacterium
b. cytoskeletal elements
c. endosymbiosis
d. membrane proliferation
7. Which of these protists is believed to have evolved
following a secondary endosymbiosis?
a. green algae
b. cyanobacteria
c. red algae
d. chlorarachniophytes
8. Protists that have a pellicle are surrounded by
______________.
a. silica dioxide
b. calcium carbonate
c. carbohydrates
d. proteins
9. Protists with the capabilities to perform photosynthesis
and to absorb nutrients from dead organisms are called
______________.
a. photoautotrophs
b. mixotrophs
c. saprobes
d. heterotrophs
10. Which of these locomotor organs would likely be the
shortest?
a. a flagellum
b. a cilium
c. an extended pseudopod
Chapter 23 | Protists 629 d. a pellicle
11. Alternation of generations describes which of the
following?
a. The haploid form can be multicellular; the
diploid form is unicellular.
b. The haploid form is unicellular; the diploid form
can be multicellular.
c. Both the haploid and diploid forms can be
multicellular.
d. Neither the haploid nor the diploid forms can be
multicellular.
12. Which protist group exhibits mitochondrial remnants
with reduced functionality?
a. slime molds
b. diatoms
c. parabasalids
d. dinoflagellates
13. Conjugation between two Paramecia produces
________ total daughter cells.
a. 2
b. 4
c. 8
d. 16
14. What is the function of the raphe in diatoms?
a. locomotion
b. defense
c. capturing food
d. photosynthesis
15. What genus of protists appears to contradict the
statement that unicellularity restricts cell size?
a. Dictyostelium
b. Ulva
c. Plasmodium
d. Caulerpa
16. An example of carbon fixation is _____________.
a. photosynthesis
b. decomposition
c. phagocytosis
d. parasitism
17. Which parasitic protist evades the host immune
system by altering its surface proteins with each
generation?
a. Paramecium caudatum
b. Trypanosoma brucei
c. Plasmodium falciparum
d. Phytophthora infestans
CRITICAL THINKING QUESTIONS
18. Describe the hypothesized steps in the origin of
eukaryotic cells.
19. Explain in your own words why sexual reproduction
can be useful if a protist’s environment changes.
20. Giardia lamblia is a cyst-forming protist parasite that
causes diarrhea if ingested. Given this information, against
what type(s) of environments might G. lamblia cysts be
particularly resistant?
21. The chlorophyte (green algae) genera Ulva and
Caulerpa both have macroscopic leaf-like and stem-like
structures, but only Ulva species are considered truly
multicellular. Explain why.
22. Why might a light-sensing eyespot be ineffective for
an obligate saprobe? Suggest an alternative organ for a
saprobic protist.
23. How does killing Anopheles mosquitoes affect the
Plasmodium protists?
24. Without treatment, why does African sleeping
sickness invariably lead to death?
630 Chapter 23 | Protists
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 24 | FUNGI
Figure 24.1 Many species of fungus produce the familiar mushroom (a) which is a reproductive structure. This (b)
coral fungus displays brightly colored fruiting bodies. This electron micrograph shows (c) the spore-bearing structures
of Aspergillus , a type of toxic fungi found mostly in soil and plants. (credit “mushroom”: modification of work by Chris
Wee; credit “coral fungus”: modification of work by Cory Zanker; credit “ Aspergillus ”: modification of work by Janice
Haney Carr, Robert Simmons, CDC; scale-bar data from Matt Russell)
Chapter Outline
24.1: Characteristics of Fungi
24.2: Classifications of Fungi
24.3: Ecology of Fungi
24.4: Fungal Parasites and Pathogens
24.5: Importance of Fungi in Human Life
Introduction
The word fungus comes from the Latin word for mushrooms. Indeed, the familiar mushroom is a reproductive structure used
by many types of fungi. However, there are also many fungi species that don't produce mushrooms at all. Being eukaryotes,
a typical fungal cell contains a true nucleus and many membrane-bound organelles. The kingdom Fungi includes an
enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi. While scientists have identified
about 100,000 species of fungi, this is only a fraction of the 1.5 million species of fungus likely present on Earth. Edible
mushrooms, yeasts, black mold, and the producer of the antibiotic penicillin, Penicillium notatum , are all members of the
kingdom Fungi, which belongs to the domain Eukarya.
Fungi, once considered plant-like organisms, are more closely related to animals than plants. Fungi are not capable of
photosynthesis: they are heterotrophic because they use complex organic compounds as sources of energy and carbon.
Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual reproduction
with alternation of generations. Most fungi produce a large number of spores , which are haploid cells that can undergo
mitosis to form multicellular, haploid individuals. Like bacteria, fungi play an essential role in ecosystems because they are
decomposers and participate in the cycling of nutrients by breaking down organic materials to simple molecules.
Fungi often interact with other organisms, forming beneficial or mutualistic associations. For example most terrestrial plants
form symbiotic relationships with fungi. The roots of the plant connect with the underground parts of the fungus forming
mycorrhizae . Through mycorrhizae, the fungus and plant exchange nutrients and water, greatly aiding the survival of
both species Alternatively, lichens are an association between a fungus and its photosynthetic partner (usually an alga).
Fungi also cause serious infections in plants and animals. For example, Dutch elm disease, which is caused by the fungus
Ophiostoma ulmi , is a particularly devastating type of fungal infestation that destroys many native species of elm ( Ulmus
sp.) by infecting the tree’s vascular system. The elm bark beetle acts as a vector, transmitting the disease from tree to tree.
Chapter 24 | Fungi 631 Accidentally introduced in the 1900s, the fungus decimated elm trees across the continent. Many European and Asiatic elms
are less susceptible to Dutch elm disease than American elms.
In humans, fungal infections are generally considered challenging to treat. Unlike bacteria, fungi do not respond to
traditional antibiotic therapy, since they are eukaryotes. Fungal infections may prove deadly for individuals with
compromised immune systems.
Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and cheese and wine making.
Many industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and
antibiotics.
24.1 | Characteristics of Fungi
By the end of this section, you will be able to:
• List the characteristics of fungi
• Describe the composition of the mycelium
• Describe the mode of nutrition of fungi
• Explain sexual and asexual reproduction in fungi
Although humans have used yeasts and mushrooms since prehistoric times, until recently, the biology of fungi was poorly
understood. Up until the mid-20th century, many scientists classified fungi as plants. Fungi, like plants, arose mostly sessile
and seemingly rooted in place. They possess a stem-like structure similar to plants, as well as having a root-like fungal
mycelium in the soil. In addition, their mode of nutrition was poorly understood. Progress in the field of fungal biology
was the result of mycology : the scientific study of fungi. Based on fossil evidence, fungi appeared in the pre-Cambrian era,
about 450 million years ago. Molecular biology analysis of the fungal genome demonstrates that fungi are more closely
related to animals than plants. They are a polyphyletic group of organisms that share characteristics, rather than sharing a
single common ancestor.
Mycologist
Mycologists are biologists who study fungi. Mycology is a branch of microbiology, and many mycologists
start their careers with a degree in microbiology. To become a mycologist, a bachelor's degree in a
biological science (preferably majoring in microbiology) and a master's degree in mycology are minimally
necessary. Mycologists can specialize in taxonomy and fungal genomics, molecular and cellular biology,
plant pathology, biotechnology, or biochemistry. Some medical microbiologists concentrate on the study
of infectious diseases caused by fungi (mycoses). Mycologists collaborate with zoologists and plant
pathologists to identify and control difficult fungal infections, such as the devastating chestnut blight, the
mysterious decline in frog populations in many areas of the world, or the deadly epidemic called white nose
syndrome, which is decimating bats in the Eastern United States.
Government agencies hire mycologists as research scientists and technicians to monitor the health of crops,
national parks, and national forests. Mycologists are also employed in the private sector by companies
that develop chemical and biological control products or new agricultural products, and by companies that
provide disease control services. Because of the key role played by fungi in the fermentation of alcohol
and the preparation of many important foods, scientists with a good understanding of fungal physiology
routinely work in the food technology industry. Oenology, the science of wine making, relies not only on the
knowledge of grape varietals and soil composition, but also on a solid understanding of the characteristics
of the wild yeasts that thrive in different wine-making regions. It is possible to purchase yeast strains isolated
from specific grape-growing regions. The great French chemist and microbiologist, Louis Pasteur, made
many of his essential discoveries working on the humble brewer’s yeast, thus discovering the process of
fermentation.
632 Chapter 24 | Fungi
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Cell Structure and Function
Fungi are eukaryotes, and as such, have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-
bound nucleus. The DNA in the nucleus is wrapped around histone proteins, as is observed in other eukaryotic cells. A
few types of fungi have structures comparable to bacterial plasmids (loops of DNA); however, the horizontal transfer of
genetic information from one mature bacterium to another rarely occurs in fungi. Fungal cells also contain mitochondria
and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus.
Unlike plant cells, fungal cells do not have chloroplasts or chlorophyll. Many fungi display bright colors arising from other
cellular pigments, ranging from red to green to black. The poisonous Amanita muscaria (fly agaric) is recognizable by its
bright red cap with white patches ( Figure 24.2 ). Pigments in fungi are associated with the cell wall and play a protective
role against ultraviolet radiation. Some fungal pigments are toxic.
Figure 24.2 The poisonous Amanita muscaria is native to temperate and boreal regions of North America. (credit:
Christine Majul)
Like plant cells, fungal cells have a thick cell wall. The rigid layers of fungal cell walls contain complex polysaccharides
called chitin and glucans. Chitin, also found in the exoskeleton of insects, gives structural strength to the cell walls of fungi.
The wall protects the cell from desiccation and predators. Fungi have plasma membranes similar to other eukaryotes, except
that the structure is stabilized by ergosterol: a steroid molecule that replaces the cholesterol found in animal cell membranes.
Most members of the kingdom Fungi are nonmotile. Flagella are produced only by the gametes in the primitive Phylum
Chytridiomycota.
Growth
The vegetative body of a fungus is a unicellular or multicellular thallus . Dimorphic fungi can change from the unicellular
to multicellular state depending on environmental conditions. Unicellular fungi are generally referred to as yeasts .
Saccharomyces cerevisiae (baker’s yeast) and Candida species (the agents of thrush, a common fungal infection) are
examples of unicellular fungi ( Figure 24.3 ).
Chapter 24 | Fungi 633 Figure 24.3 Candida albicans is a yeast cell and the agent of candidiasis and thrush. This organism has a similar
morphology to coccus bacteria; however, yeast is a eukaryotic organism (note the nucleus). (credit: modification of
work by Dr. Godon Roberstad, CDC; scale-bar data from Matt Russell)
Most fungi are multicellular organisms. They display two distinct morphological stages: the vegetative and reproductive.
The vegetative stage consists of a tangle of slender thread-like structures called hyphae (singular, hypha ), whereas the
reproductive stage can be more conspicuous. The mass of hyphae is a mycelium (Figure 24.4 ). It can grow on a surface,
in soil or decaying material, in a liquid, or even on living tissue. Although individual hyphae must be observed under a
microscope, the mycelium of a fungus can be very large, with some species truly being “the fungus humongous.” The giant
Armillaria solidipes (honey mushroom) is considered the largest organism on Earth, spreading across more than 2,000 acres
of underground soil in eastern Oregon; it is estimated to be at least 2,400 years old.
Figure 24.4 The mycelium of the fungus Neotestudina rosati can be pathogenic to humans. The fungus enters through
a cut or scrape and develops a mycetoma, a chronic subcutaneous infection. (credit: CDC)
Most fungal hyphae are divided into separate cells by endwalls called septa (singular, septum )(Figure 24.5 a, c ). In most
phyla of fungi, tiny holes in the septa allow for the rapid flow of nutrients and small molecules from cell to cell along
the hypha. They are described as perforated septa. The hyphae in bread molds (which belong to the Phylum Zygomycota)
are not separated by septa. Instead, they are formed by large cells containing many nuclei, an arrangement described as
coenocytic hyphae (Figure 24.5 b).
634 Chapter 24 | Fungi
This OpenStax book is available for free at http://cnx.org/content/col11448/1.10 Figure 24.5 Fungal hyphae may be (a) septated or (b) coenocytic (coeno- = "common"; -cytic = "cell") with many nuclei
present in a single hypha. A bright field light micrograph of (c) Phialophora richardsiae shows septa that divide the
hyphae. (credit c: modification of work by Dr. Lucille Georg, CDC; scale-bar data from Matt Russell)
Fungi thrive in environments that are moist and slightly acidic, and can grow with or without light. They vary in
their oxygen requirement. Most fungi are obligate aerobes , requiring oxygen to survive. Other species, such as the
Chytridiomycota that reside in the rumen of cattle, are are obligate anaerobes , in that they only use anaerobic respiration
because oxygen will disrupt their metabolism or kill them. Yeasts are intermediate, being faculative anaerobes . This means
that they grow best in the presence of oxygen using aerobic respiration, but can survive using anaerobic respiration when
oxygen is not available. The alcohol produced from yeast fermentation is used in wine and beer production.
Nutrition
Like animals, fungi are heterotrophs; they use complex organic compounds as a source of carbon, rather than fix carbon
dioxide from the atmosphere as do some bacteria and most plants. In addition, fungi do not fix nitrogen from the
atmosphere. Like animals, they must obtain it from their diet. However, unlike most animals, which ingest food and then
digest it internally in specialized organs, fungi perform these steps in the reverse order; digestion precedes ingestion. First,
exoenzymes are transported out of the hyphae, where they process nutrients in the environment. Then, the smaller molecules
produced by this external digestion are absorbed through the large surface area of the mycelium. As with animal cells, the
polysaccharide of storage is glycogen, rather than starch, as found in plants.
Fungi are mostly saprobes (saprophyte is an equivalent term): organisms that derive nutrients from decaying organic
matter. They obtain their nutrients from dead or decomposing organic matter: mainly plant material. Fungal exoenzymes
are able to break down insoluble polysaccharides, such as the cellulose and lignin of dead wood, into readily absorbable
glucose molecules. The carbon, nitrogen, and other elements are thus released into the environment. Because of their
varied metabolic pathways, fungi fulfill an important ecological role and are being investigated as potential tools in
bioremediation. For example, some species of fungi can be used to break down diesel oil and polycyclic aromatic
hydrocarbons (PAHs). Other species take up heavy metals, such as cadmium and lead.
Some fungi are parasitic, infecting either plants or animals. Smut and Dutch elm disease affect plants, whereas athlete’s
foot and candidiasis (thrush) are medically important fungal infections in humans. In environments poor in nitrogen, some
fungi resort to predation of nematodes (small non-segmented roundworms). Species of Arthrobotrys fungi have a number
of mechanisms to trap nematodes. One mechanism involves constricting rings within the network of hyphae. The rings
swell when they touch the nematode, gripping it in a tight hold. The fungus penetrates the tissue of the worm by extending
specialized hyphae called haustoria . Many parasitic fungi possess haustoria, as these structures penetrate the tissues of the
host, release digestive enzymes within the host's body, and absorb the digested nutrients.
Chapter 24 | Fungi 635 Reproduction
Fungi reproduce sexually and/or asexually. Perfect fungi reproduce both sexually and asexually, while the so-called