Jay Phelan
What Is Life? A Guide To Biology
Second Edition
CHAPTER 13
Evolution and Diversity
Among the Microbes
© 2012 W. H. Freeman and Company
FIGURE 13-1 The most abundant organisms on earth are too small to see
FIGURE 13-1 The most abundant organisms on earth are too small to see
FIGURE 13-1 The most abundant organisms on earth are too small to see
FIGURE 13-1 The most abundant organisms on earth are too small to see
FIGURE 13-1 The most abundant organisms on earth are too small to see
Although almost all microbes are invisible to the naked eye, they vary tremendously in size.
20x larger
Influenza virus
100 nm
25x larger
Escherichia coli
2 μm
20x larger
Euglena gracilis
50 μm
Amoeba dubia
1 mm
If an influenza virus were the size of
a pinhead, an amoeba would be the
size of an oak tree.
Escherichia coli (inset), a
bacterium, lives in the human
intestine.
Thermus aquaticus (inset), a
bacterium, lives in geothermal
pools that can reach
temperatures greater than
160° F.
Halobacteria (inset) are
archaeons that live in
extremely salty
environments, such as
the Great Salt Lake.
Microbes live in nearly every kind of environment, including
water at temperatures of up to 750° F and as low as 5° F!
Microbial cells
that live in and
on you
Human cells

Microbes are simple, but they do everything that
multicellular organisms do.

They can live anywhere, from moderate to extreme
environments.

There are millions of different kinds of microbes on
earth, in enormous numbers.
Take-home message
13.1
DOMAIN BACTERIA
Neisseria meningitidis, a
bacterium that can cause
meningitis
DOMAIN ARCHAEA
Haloferax mediterranei,
an extremely halophilic archaean
DOMAIN EUKARYA
A giant amoeba, from the
genus Pelomyxa
Microbes are found in all three
domains of life—and beyond.
Viruses aren’t truly living
organisms and they are
not classified into any of
the three domains.
Bacteriophage virus

Microbes are grouped together only because they are
small, not because of evolutionary relatedness.

They occur in all three domains of life, and also
include the viruses, which are not included in any of
the domains.
Take-home message
13.2
COCCI
Spherical bacteria
BACILLI
Rod-shaped bacteria
SPIRILLI
Spiral-shaped bacteria
Bacterial species are
commonly classified by
their shape.
Capsule
Cell wall
Plasma membrane
Chromosome (DNA)
Plasmid (DNA)
Pili
Cytoplasm
Ribosomes
Flagellum
Some bacteria can be identified
by looking at the colors and
shapes of their colonies.
GRAM-POSITIVE BACTERIA
The glycoprotein layer is on the
outside of the cell wall and can
be stained with purple dye.
GRAM-NEGATIVE BACTERIA
The glycoprotein layer lies
beneath an additional
membrane and cannot be
stained with the dye.
Gram-negative bacteria—due to their cell
membrane composition—are resistant to penicillin.
FIGURE 13-7 Binary fission
FIGURE 13-7 Binary fission
FIGURE 13-7 Binary fission
FIGURE 13-7 Binary fission
Bacterium cell
Plasmids
(DNA)
Chromosome
(DNA)
REPLICATION
Exact copies of the cell’s chromosomal
and plasmid DNA are created.
Cell elongates and
begins to pinch in two.
Daughter cells
are formed.
Fission can be extremely fast—in
less than 12 hours, a single E. coli
could give rise to a population of
20 billion cells (three times the
number of humans on earth)!

Bacteria are efficient single-celled organisms, with an
envelope surrounding the cytoplasm, which contains
the DNA (they have no nuclei and no intracellular
organelles).

Bacterial cells undergo binary fission, and a single
cell can grow into a colony of cells.
Take-home message
13.3
CONJUGATION
A bacterium transfers a copy of
some or all of its DNA to
another bacterium, giving the
second bacterium genetic
information it did not have
before.
Donor
bacterium
Recipient
bacterium
TRANSDUCTION
A virus containing pieces of
bacterial DNA inadvertently
picked up from its previous host
infects a new bacterium, and
passes new bacterial genes to
the bacterium.
Virus
Recipient
bacterium
TRANSFORMATION
A bacterium can take up DNA—
potentially including alleles it did
not carry—from its surroundings
(usually from bacteria that have
died).
DNA
fragments
Recipient
bacterium

Bacteria sometimes carry the genes for specialized
traits on small DNA molecules called plasmids that
can be transferred from one bacterial cell to another
by conjugation.

DNA can also be transferred laterally between
bacterial cells by transduction or transformation.
Take-home message
13.4

Bacteria grow rapidly.

They have efficiently organized chromosomes—
genes are organized in groups with related functions
and virtually all the DNA codes for proteins.
Take-home message
13.4
CHEMOORGANOTROPHS
Feed on organic molecules
CHEMOLITHOTROPHS
Feed on inorganic molecules
(Shown here: a stream in Spain
orange with oxidized iron
minerals.)
PHOTOAUTOTROPHS
Use energy from sunlight to
produce glucose via
photosynthesis
Bacteria are resourceful and can extract food
from a huge range of sources: the sun, inorganic
molecules in your drainage pipes, and even your
shower curtain/door!

Some bacteria eat organic molecules, some eat
minerals, and still other bacteria carry out
photosynthesis.

About 2.6 billion years ago, the photosynthesizing
bacteria were responsible for the first appearance of
free oxygen in the Earth's atmosphere.
Take-home message
13.5
Many bacteria are beneficial. Those living in
yogurt, for example, can take up residence in
your digestive tract and improve your extraction
of nutrients from food.

Your body fights bacteria with bacteria.

A disease-causing bacterium must colonize your
body before it can make you sick, and your body is
already covered with harmless bacteria.

If the population of harmless bacteria is dense
enough, it will prevent invading bacteria from gaining
a foothold.
Take-home message
13.6
By mapping the pattern of
deaths from cholera, Dr.
John Snow was able to
identify the Broad Street
water pump as the source
of the infection.
Deaths from cholera (size of circle
proportionate to number of deaths)
Street pump
Streptococcus pyogenes is usually harmless,
but some strains are responsible for strep
throat, scarlet fever, and necrotizing fasciitis
(flesh-eating bacteria).

Some bacteria always cause disease and others do
no harm except under certain conditions.

For example, Streptococcus pyogenes can be
harmless, but under some conditions it releases
toxins that are responsible for strep throat, scarlet
fever, and necrotizing fasciitis (caused by the flesheating strains).
Take-home message
13.7
1
INFECTION
Patient A and Patient B both have an infection caused by a
harmful strain of bacteria.
Harmful bacteria
Harmless bacteria
Patient A
Patient B
2
ANTIBIOTICS
Both patients are prescribed an antibiotic to treat the infection,
which reduces the initial number of harmful bacteria.
Patient A
Patient B
3
OUTCOMES
a Patient A continues
to take the antibiotic
as prescribed until
all of the pills have
been consumed.
Patient A
Harmful bacterial population is
significantly reduced (and can be
held in check by competition with
other, harmless bacteria).
b Patient B stops
taking the antibiotic
before finishing all of
the prescribed
amount.
Patient B
The harmful bacterial cells still
alive are the most resistant to the
antibiotic and can proliferate,
leading to future health problems.
Livestock are given antibiotics to
prevent diseases easily spread in
crowded living conditions.
Agriculture in the United States uses about 25
million pounds of antibiotics each year—about
eight times more than is used for all human
medicine!

Microbes routinely evolve resistance to antibiotics.

The genes that allow bacteria to combat antibiotics
are located on plasmids, and plasmid transfer allows
an antibiotic-resistant bacterium to pass that
resistance to other bacteria.
Take-home message
13.8

Excessive use of antibiotics in medicine and
agriculture has made several pathogenic bacteria
resistant to every known antibiotic, and infections
caused by these bacteria are nearly impossible to
treat.
Take-home
message 13.8
BACTERIUM
VIRUS
• Gonorrhea
Often none; sometimes painful urination,
genital discharge, or irregular menstruation
Several antibiotics can successfully cure gonorrhea;
however, drug-resistant strains are increasing.
• Syphilis
Often no symptoms for years; eventual sores,
skin rash, and if untreated, organ damage
Penicillin, an antibiotic, can cure a person in the early
stages of syphilis.
• Chlamydia
Often none; sometimes painful urination,
genital discharge
Chlamydia can be easily treated and cured with
antibiotics.
• HIV/AIDS
Initial symptoms range from none to flu-like; late
stages involve severe infections and death
Currently no cure. Antiretroviral treatment can slow
progression. Drug-resistant strains occur.
• Genital herpes
Often none; outbreaks include sores on
genitals, flu-like symptoms
Currently no cure. Antiviral medications can shorten
and prevent outbreaks.
• Human papilloma Often none; some types can lead to genital
warts, others can cause cervical cancer
virus (HPV)
A vaccine prevents HPV, and is recommended for girls age
11–12. Warts and cancerous lesions can be removed.
• Trichomoniasis
Painful urination and/or vaginal discharge in
women; often no symptoms in men
Trichomoniasis can usually be cured with prescription
drugs.
• Yeast infections
Genital itching or burning, and/or vaginal
discharge in women; genital itching in men
Yeast infections can usually be cured with antifungal
suppositories or creams.
• Crab lice
Visible lice eggs or lice crawling or attached to
pubic hair; itching in the pubic and groin area
Crab lice can be treated with over-the-counter lotions.
PROTIST
FUNGUS
ARTHROPOD

Sexually transmitted diseases (STDs) are caused by
a variety of organisms, including bacteria, viruses,
protists, fungi, and arthropods.
Take-home
message 13.9

Worldwide, more than 300 million people are newly
infected each year.

The effects of being infected with an STD range from
nonexistent to mild to extreme discomfort, sterility, or
even death.
Take-home
message 13.9
Archaea look very much like bacteria. But closer
inspection—of their physiology, biochemistry,
and DNA—reveals them to be profoundly
different from all bacteria.

Archaea show a set of characteristics that places
them between bacteria and eukaryotes on the tree of
life.
Take-home message
13.10

Archaea and bacteria may look similar, but they have
large and significant differences in their DNA
sequences, as well as differences in their plasma
membranes, cell walls, and flagella.

Furthermore, neither archaea nor bacteria resemble
eukarya in one key way: only eukarya have a distinct
cell nucleus and nuclear membrane.
Take-home
message 13.10
Archaea in your intestine break down a chemical
bond found in beans (a bond humans cannot
break)...but the process generates gas, which
can cause discomfort as it tries to escape.

Archaeans can tolerate extreme physical and
chemical conditions that are impossible for most
other living organisms, but they also live in moderate
conditions and even in the human intestine.
Take-home message
13.11

Archaea are hard to study because many require
extreme heat or pressure to grow, and these
conditions are not easy to provide in a laboratory.

But the ability of archaea to grow in such extreme
conditions makes them potentially valuable for
industrial and environmental purposes.
Take-home
message 13.12
In these ancient fossilized eukaryotes,
organelles are visible.
ANIMAL-LIKE PROTISTS
Some protists, such as
Trichomonas vaginalis shown
here, move around and hunt
for prey like an animal.
FUNGI-LIKE PROTISTS
Some protists, such as the
plasmodial slime mold shown
here, live as heterotrophs and
form sheet-like colonies of
cells like a fungus.
PLANT-LIKE PROTISTS
Some protists, such as the
kelp forest shown here, are
multicellular and
photosynthetic like a plant.
1
Following the bite of a
Plasmodium-infected
mosquito, malariacausing protists take up
residence in healthy
red blood cells.
Plasmodium parasite
infecting a red blood cell
2
Once inside a red blood
cell, Plasmodium cells
modify the cell's surface
proteins, making it
difficult for the immune
system to fight the
malarial infection.
RESISTANCE TO MALARIA
In individuals with sickle-cell
trait, the sickle shape of some
red blood cells makes the cells
inhospitable to the protist. This
makes these individuals
resistant to malaria.
Capsid (container
made of protein)
Genetic material
(DNA or RNA)
Plasma membrane
(envelope)
Glycoproteins
Enveloped viruses wrap
themselves in a bit of the
plasma membrane of the
host cell as they are
released.
ENVELOPED VIRUS
Enclosed in the plasma
membrane of a host cell
NON-ENVELOPED VIRUS
Enclosed only by its capsid
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
FIGURE 13-25 Making more viruses
Virus
1
1 After the virus binds to the host
2
3
4
5
cell's membrane, the viral DNA
is taken into the cell.
Viral DNA is replicated into
dozens of new copies, using
the host's metabolic machinery
and energy.
Viral mRNA is transcribed from
the viral DNA.
New viral proteins are
synthesized, again using the
host's protein-production
molecules.
The new viral DNA and
proteins assemble, forming
many new virus particles.
Host cell
5
Host nucleus
2
Viral DNA
Replicated
viral DNA
3
4
Viral mRNA
Viral proteins
Because they are dependent on their hosts’
metabolic machinery for replication, viruses
are not considered “living.”

A virus is not alive, but it can carry out some of the
same functions as living organisms, provided that it
can get inside a cell.
Take-home message
13.16

A virus takes over the protein-making machinery of
the host cell to produce more viral genetic material
(RNA or DNA) and more viral protein.

The viral proteins and genetic material are
assembled into new virus particles and released from
the cell.
Take-home message
13.16

Many diseases are caused by viruses.

DNA viruses are relatively stable because DNA
replication enzymes check for errors and correct
them during replication.
Take-home message
13.17

RNA viruses change quickly because RNA replication
enzymes do not have error- checking mechanisms.
Take-home message
13.17
SURFACE GLYCOPROTEINS
• Bind to receptors on the
surface of the host cell and
allow the virus to enter
• Allow the virus to break
free from the host cell
Surface glycoproteins are
the “keys” that allow a virus
into and out of a host cell.
Viruses that infect birds don’t
bind well to glycoproteins in
human cells, making it difficult for
bird viruses to infect humans.

Glycoproteins on the surfaces of viruses determine
what cells they can invade.

Most viruses infect just one species, or only a few
closely related species, and enter only one kind of
cell in that species.
Take-home message
13.18
Viruses that infect birds don’t bind well to glycoproteins in human
cells, making it difficult for bird viruses to infect humans.
However, a virus that infects humans and a virus that infects birds can
meet in a pig cell, replicate, and get packaged together into a new
virus capable of infecting humans.
HIV is a virus that carries its genetic
instructions in the form of RNA rather
than DNA.
RNA (two identical strands)
Reverse transcriptase
Surface glycoproteins
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
FIGURE 13-29 HIV infection
Host cell
Viral
RNA
Reverse
transcriptase
1
An enzyme carried within the HIV
particle converts the viral RNA into
DNA once inside the infected cell.
(Making DNA from RNA is like
transcription in reverse, so the
enzyme is called reverse
transcriptase.)
2
The newly produced DNA, based on
the code carried by the HIV particles,
is inserted into the host's DNA.
3
The host cell then transcribes the
genes from HIV, much like it
transcribes other genes. But these
genes code for the production of
new virus particles.
4
The new virus particles are
assembled and released from the
host cell.
Viral DNA
Host nucleus
Host
DNA
New viral
RNA
New viral
proteins

HIV is especially difficult to control.

Mutations change the properties of the virus so that it
is hard for the immune system to recognize it, and
they produce variants that are resistant to the drugs
being used to treat the HIV infection.
Take-home message
13.19
1. What can you conclude from this figure?
2. How many human cells are there in a
human?
3. How many microbial cells are there in a human?
4. How can bacterial cells outnumber human
cells in a human, yet a person still looks
human rather than bacterial?
5. How were the data obtained for the graph?
Are they from an experiment? If so, what
additional information would have been
useful?
6. Create two alternative ways of conveying the
information in this figure. What are the relative
strengths and weaknesses of your graphs
compared with this figure?