Download Lecture Presentation to accompany Principles of Life

19
Bacteria, Archaea, and
Viruses
Chapter 19 Bacteria, Archaea, and Viruses
Key Concepts
• 19.1 Life Consists of Three Domains That
Share a Common Ancestor
• 19.2 Prokaryote Diversity Reflects the
Ancient Origins of Life
• 19.3 Ecological Communities Depend on
Prokaryotes
• 19.4 Viruses Have Evolved Many Times
Chapter 19 Opening Question
How do Vibrio populations detect when
they are dense enough to produce
bioluminescence?
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
All organisms have:
• Plasma membranes and ribosomes
• Metabolic pathways (e.g., glycolysis)
• Conservative DNA replication
• DNA that encodes proteins
Shared features indicate that all life is related,
but major differences have also evolved.
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Three domains of life:
• Bacteria—prokaryotes
• Archaea—prokaryotes
• Eukarya—eukaryotes
Figure 19.1 The Three Domains of the Living World
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Prokaryotes differ from eukaryotes.
• All are unicellular
• Divide by binary fission, not mitosis
• DNA is often circular, not in a nucleus
• No membrane-enclosed organelles
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Genetic studies show that the three domains had
a single common ancestor.
Some eukaryote genes are most closely related
to those of archaea, while others are most
closely related to those of bacteria.
Mitochondria and chloroplasts of eukaryotes
originated through endosymbiosis with a
bacterium.
Table 19.1 The Three Domains of Life on Earth
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Study of prokaryotes was not possible until
microscopes were developed.
Before DNA sequencing, classification was
based on phenotypic characters such as
shape, color, motility, nutrition, and cell wall
structure.
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Most bacteria cell walls contain peptidoglycan,
which is unique to bacteria.
Antibiotics target peptidoglycan because
eukaryote cells don’t have it, thus there is no
harm to human cells.
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Bacteria can be grouped by the Gram stain
response, which is based on differences in cell
wall structure:
Gram-positive bacteria appear blue to purple.
Gram-negative bacteria appear pink to red.
Figure 19.2 The Gram Stain and the Bacterial Cell Wall (Part 1)
Figure 19.2 The Gram Stain and the Bacterial Cell Wall (Part 2)
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Common bacteria cell shapes:
• Sphere—coccus (plural cocci), occur singly
or in plates, blocks, or clusters
• Rod—bacillus (plural bacilli)
• Spiral or helical—helix (plural helices)
Rods and helical shapes may form chains or
clusters.
Other bacterial shapes form filaments and
branched filaments.
Figure 19.3 Bacterial Cell Shapes
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Sequencing of ribosomal RNA (rRNA) genes is
useful for phylogenetic studies because:
• rRNA was present in the common ancestor of
all life.
• All free-living organisms have rRNA.
• Lateral transfer of rRNA genes among distantly
related species is unlikely.
• rRNA has evolved slowly.
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Whole genome sequencing has revealed that
even distantly related prokaryotes sometimes
exchange genetic material.
Transformation, conjugation, and transduction
allow exchange of genetic information between
prokaryotes without reproduction.
In lateral gene transfer, genes move “sideways”
from one species to another. When sequenced,
gene trees will not match the organismal tree.
Figure 19.4 Lateral Gene Transfer Complicates Phylogenetic Relationships
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Genes that result in new adaptations that confer
higher fitness are most likely to be transferred.
Genes for antibiotic resistance are often
transferred among bacterial species.
Concept 19.1 Life Consists of Three Domains
That Share a Common Ancestor
Many prokaryote species, and perhaps whole
clades, have not been described by biologists.
Many have resisted efforts to grow them in pure
culture.
Biologists now examine gene sequences
collected from random samples of the
environment. Many new sequences imply there
are thousands more prokaryotic species.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Prokaryotes are the most successful organisms
on Earth in terms of number of individuals.
The number of prokaryotes in the ocean is
perhaps 100 million times as great as the
number of stars in the visible universe.
They are found in every type of habitat on Earth.
We will describe eight bacterial groups.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Low-GC Gram-positives (Firmicutes)
Low ratio of G-C to A-T base pairs in DNA.
Some are gram-negative, and some have no cell
wall.
Some produce heat-resistant endospores that
can survive unfavorable conditions. Some can
survive for 1,000 years.
Includes Clostridium and Bacillus.
Figure 19.5 A Structure for Waiting Out Bad Times
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Bacillus anthracis produces an exotoxin that
causes anthrax. The endospores have been
used as a bioterrorism agent.
Staphylococcus (staphylococci) are abundant
on skin and cause boils and other skin
problems. S. aureus can also cause
respiratory, intestinal, and wound infections.
Figure 19.6 Staphylococci
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Mycoplasmas have no cell wall, are extremely
small, and have a very small genome.
They have less than half as much DNA as
other prokaryotes, which may represent the
minimum amount of DNA needed for a living
cell.
Figure 19.7 Tiny Cells
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
High-GC Gram-positives (Actinobacteria)
Higher ratio of G-C to A-T base pairs.
Branched filaments; some form reproductive
spores at filament tips.
Most antibiotics are from this group.
Mycobacterium tuberculosis causes
tuberculosis; oldest know human pathogen.
Figure 19.8 Actinomycetes Are High-GC Gram-Positives
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Hyperthermophilic bacteria
Live at extreme high temperatures
(extremophiles)—hot springs, volcanic vents,
underground oil reservoirs.
High temperatures may have been the ancestral
condition on Earth when prokaryotes evolved.
Monophyly of this group is not well established.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Hadobacteria
Also extreme thermophiles.
Deinococcus survive cold as well as hot
temperatures and are resistant to radiation.
They can consume nuclear waste.
Thermus aquaticus was isolated from a hot
spring; source of the thermally stable DNA
polymerase used in PCR.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Cyanobacteria
Photosynthetic; have blue-green pigments.
Many species fix nitrogen.
Chloroplasts of eukaryotes are derived from an
endosymbiotic cyanobacterium.
Some colonies differentiate into vegetative
cells, spores, and heterocysts specialized for
N-fixation.
Figure 19.9 Cyanobacteria (Part 1)
Figure 19.9 Cyanobacteria (Part 2)
Figure 19.9 Cyanobacteria (Part 3)
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Spirochetes
Gram-negative; motile
Unique axial filaments (modified flagella) that
rotate
Many are human parasites, some are pathogens
(syphilis, Lyme disease), others are free living.
Figure 19.10 Spirochetes Get Their Shape from Axial Filaments (Part 1)
Figure 19.10 Spirochetes Get Their Shape from Axial Filaments (Part 2)
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Chlamydias
Can live only as parasites in cells of other
organisms.
Gram-negative; extremely small
Can take up ATP from host cell with translocase
Complex life cycle with two forms—elementary
bodies and reticulate bodies
Figure 19.11 Chlamydias Change Form during Their Life Cycle
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Proteobacteria: largest group of bacteria
Mitochondria of eukaryotes were derived from a
proteobacterium by endosymbiosis.
Some are photoautotrophs that use light energy
to metabolize sulfur; some are N-fixers
(Rhizobium).
Escherichia coli is one of the most studied
organisms on Earth.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Agrobacterium tumefaciens causes crown gall
disease of plants and has a plasmid used in
recombinant DNA studies.
The proteobacteria include many pathogens—
cholera, bubonic plague, salmonella.
Figure 19.12 Proteobacteria Include Human Pathogens
Figure 19.13 Crown Gall
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Separation of the Archaea domain from bacteria
and eukaryotes is based on genome
sequencing.
Many archaea live in extreme habitats—high
temperatures, low oxygen, high salinity,
extreme pH.
Many others are common in soil and in the
oceans.
Figure 19.14 What Is the Highest Temperature Compatible with Life? (Part 1)
Figure 19.14 What Is the Highest Temperature Compatible with Life? (Part 2)
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Archaea are divided into two main groups,
Euryarcheota and Crenarcheota
Two recently discovered groups:
• Korarchaeota (known only from DNA in hot
springs)
• Nanoarchaeota, a parasite on cells of a
crenarchaeote in deep sea hydrothermal vents
All lack peptidoglycan in the cell walls and have
unique lipids in the cell membranes.
Figure 19.18 A Nanoarchaeote Growing in Mixed Culture with a Crenarchaeote
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Bacterial and eukaryotic membranes have lipids
with fatty acids connected to glycerol by ester
linkages.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Archaeal membranes have lipids with fatty acids
linked to glycerol by ether linkages.
This is a synapomorphy of archaea.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Some archaeal lipids have glycerol at both ends
and form lipid monolayers.
Others have lipid bilayers.
Figure 19.15 Membrane Architecture in Archaea
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Most Crenarcheota are thermophilic and/or
acidophilic (acid loving).
Sulfolobus lives in hot sulfur springs (70–75°C,
pH 2 to 3).
They can still maintain an internal pH of 5.5 to 7.
Figure 19.16 Crenarchaeotes Like It Hot
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Some Euryarcheota are methanogens.
CH4 is produced by reducing CO2; they are
obligate anaerobes.
Methanogens release 2 billion tons of methane
per year. Many live in the guts of grazing
mammals, termites, and cockroaches.
Increased cattle farming and rice growing
contributes methane to the atmosphere.
Concept 19.2 Prokaryote Diversity Reflects the Ancient
Origins of Life
Extreme halophiles (salt lovers) have pink
carotenoid pigments.
Live in the most salty, most alkaline
environments on Earth.
Some have a light-absorbing molecule, microbial
rhodopsin, to trap light energy and form ATP.
Figure 19.17 Extreme Halophiles
Concept 19.3 Ecological Communities Depend on Prokaryotes
Many prokaryotes form complex communities.
Biofilms—cells bind to a solid surface and
secrete a sticky polysaccharide matrix that
traps other cells.
Cells in biofilms are hard to kill.
Can form on any surface, including contact
lenses, artificial joint replacements, metal
pipes.
Dental plaque and stromatolites are biofilms.
Figure 19.19 Forming a Biofilm (Part 1)
Figure 19.19 Forming a Biofilm (Part 2)
Concept 19.3 Ecological Communities Depend on Prokaryotes
The long evolutionary history of prokaryotes has
led to a great diversity of metabolic pathways.
They have evolved huge variation in use or
nonuse of oxygen, energy and carbon sources,
and waste products produced.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Anaerobes do not use oxygen as an electron
acceptor in respiration.
Obligate anaerobes—oxygen is poisonous.
Aerotolerant anaerobes—not damaged by
oxygen.
Facultative anaerobe—use both aerobic and
anaerobic metabolic pathways.
Obligate aerobes—require oxygen.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Nutritional categories:
• Photoautotrophs perform photosynthesis; use
CO2 as carbon source.
Cyanobacteria use chlorophyll a and produce
O2.
Others use bacteriochlorophyll and produce
sulfur; H2S is the electron donor.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Bacteriochlorophyll absorbs longer wavelengths
than chlorophyll.
Bacteria using this pigment can grow in deeper
water under dense layers of algae, using light
that is not absorbed by the algae.
Figure 19.20 Bacteriochlorophyll Absorbs Long-Wavelength Light
Concept 19.3 Ecological Communities Depend on Prokaryotes
• Photoheterotrophs use light as an energy
source, but get carbon from organic
compounds made by other organisms.
Sunlight provides the ATP through
photophosphorylation.
Concept 19.3 Ecological Communities Depend on Prokaryotes
• Chemolithotrophs (chemoautotrophs) get
energy by oxidizing inorganic substances and
use it to fix carbon.
Inorganic compounds oxidized include ammonia,
nitrite, hydrogen gas, hydrogen sulfide, sulfur,
and other materials.
Concept 19.3 Ecological Communities Depend on Prokaryotes
• Chemoheterotrophs get both energy and
carbon from organic compounds that have
been synthesized by other organisms.
Most known bacteria and archaea are
chemoheterotrophs—as are all animals, fungi,
and many protists.
Table 19.2 How Organisms Obtain Their Energy and Carbon
Concept 19.3 Ecological Communities Depend on Prokaryotes
Prokaryotes play a major role in the cycling of
elements.
Many are decomposers: they metabolize organic
compounds in dead organic material. The
inorganic products, such as CO2, are returned
to the environment.
Other prokaryotes oxidize inorganic compounds
and also play key roles in element cycling.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Denitrifiers:
Bacteria that use nitrate (NO3–) as an electron
acceptor in place of O2 in anaerobic conditions.
They release N2 to the atmosphere.
They play a key role in nitrogen cycling.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Nitrogen fixers:
Convert N2 to ammonia. Ammonia is a form of
nitrogen that is useable by organisms.
Nitrogen fixation is vital to life and is done only
by certain prokaryote species.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Nitrifiers:
Chemolithotrophic bacteria that oxidize ammonia
to nitrate.
Nitrate is the form of nitrogen most easily used
by many plants.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Many prokaryotes live on or in eukaryotic
organisms (e.g., nitrogen fixers that live in plant
root nodules).
Animals have many prokaryotes in their
digestive tracts.
Bacteria in the rumen of cattle produce the
enzyme needed to digest cellulose.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Humans have thousands of bacterial species on
their skin and in their guts. Gut bacteria help
digest and absorb nutrients and produce
vitamins.
Only a small percentage of bacteria are
pathogens.
Concept 19.3 Ecological Communities Depend on Prokaryotes
Late 19th century—studies began to show the
microbial basis of some diseases.
Koch’s postulates were rules for establishing
that a particular microorganism causes a
particular disease.
These rules were used to show that ulcers are
caused by a bacterium Helicobacter pylori.
Figure 19.21 Satisfying Koch’s Postulates (Part 1)
Figure 19.21 Satisfying Koch’s Postulates (Part 2)
Concept 19.3 Ecological Communities Depend on Prokaryotes
In spite of the many defense mechanisms of
potential hosts, some bacteria are very
successful pathogens.
Because they form biofilms, pathogens can be
hard to combat.
Consequences of bacterial infections depend on
invasiveness of the pathogen (ability to
multiply in host’s body) and its toxigenicity
(ability to produce toxins).
Concept 19.3 Ecological Communities Depend on Prokaryotes
Endotoxins are released when certain Gramnegative bacteria lyse (burst); rarely fatal; they
cause fever, vomiting, and diarrhea.
Examples: Salmonella and Escherichia
Exotoxins are released by living bacteria; highly
toxic, often fatal.
Examples: tetanus (Clostridium tetani), cholera
(Vibrio cholerae), bubonic plague (Yersinia
pestis), anthrax (Bacillus anthracis), botulism
(Clostridium botulinum).
Concept 19.4 Viruses Have Evolved Many Times
Although viruses are not cellular, they have
many characteristics of living organisms.
Virus phylogeny is difficult to resolve: small
genomes restrict phylogenetic analyses; rapid
mutation and evolution rates cloud evolutionary
relationships; there are no fossils.
Instead, viruses are grouped based on genome
structure.
Concept 19.4 Viruses Have Evolved Many Times
Viruses are obligate cellular parasites, but many
may have once been cellular components.
They may be “escaped” components cells that
now evolve independently of their hosts.
Concept 19.4 Viruses Have Evolved Many Times
Negative-sense single-stranded RNA viruses:
Negative-sense RNA—the complement of
mRNA.
They can make mRNA from their negative-sense
RNA genome.
These viruses probably arose by cellular escape
many times independently across the tree of
life.
Includes viruses that cause measles, mumps,
rabies, and influenza.
Figure 19.22 Viruses Are Diverse (Part 1)
Concept 19.4 Viruses Have Evolved Many Times
Positive-sense single-stranded RNA viruses:
The most abundant and diverse group; includes
mosaic viruses of crop plants, polio, hepatitis
C, and the common cold.
They also appear to have evolved multiple times
across the tree of life from different groups of
cellular ancestors.
Figure 19.22 Viruses Are Diverse (Part 2)
Figure 19.23 Mosaic Viruses Are a Problem for Agriculture
Concept 19.4 Viruses Have Evolved Many Times
RNA retroviruses:
Single-stranded RNA; probably evolved as
escaped cellular components.
Regenerate themselves by reverse transcription.
DNA is produced and integrated into the host
genome, where it is replicated along with host’s
DNA.
Only infect vertebrates; includes HIV, and some
are associated with various cancers.
Figure 19.22 Viruses Are Diverse (Part 3)
Concept 19.4 Viruses Have Evolved Many Times
Double-stranded RNA viruses:
May have evolved repeatedly from singlestranded RNA ancestors.
Cause many plant diseases and infant diarrhea
in humans.
Concept 19.4 Viruses Have Evolved Many Times
Double-stranded DNA viruses:
May represent highly reduced parasitic
organisms that have lost their cellular structure
and ability to survive as free-living species.
Some have genomes as large as parasitic
bacteria.
Includes bacteriophage, smallpox, and herpes
viruses.
Figure 19.22 Viruses Are Diverse (Part 4)
Figure 19.22 Viruses Are Diverse (Part 5)
Figure 19.22 Viruses Are Diverse (Part 6)
Answer to Opening Question
Bacteria release chemical substances that are
sensed by others of the same species.
As population increases, concentration of
chemical signal builds up. Bacteria then start
activities such as forming a biofilm (quorum
sensing).
When populations are dense enough, Vibrio
produce bioluminescence, which attracts fish
that eat the phytoplankton on which the
bacteria are growing, which gets the bacteria
into a new host.