Bacteria and Archaea:
The Prokaryotic Domains
27 Bacteria and Archaea: The Prokaryotic Domains
• Why Three Domains?
• General Biology of the Prokaryotes
• Prokaryotes in Their Environments
• Prokaryote Phylogeny and Diversity
• The Bacteria
• The Archaea
27 Why Three Domains?
• Biologists now categorize all life into three domains:
Bacteria, Archaea, and Eukarya.
• Members of all three domains have certain
characteristics in common:
They conduct glycolysis.
They replicate their DNA semiconservatively.
They have DNA that encodes polypeptides.
They produce polypeptides by transcription and
translation and use the same genetic code.
They have plasma membranes and ribosomes.
27 Why Three Domains?
• All three domains had a single common ancestor.
• Present-day Archaea share a more recent
common ancestor with eukaryotes than they do
with bacteria.
• The common ancestor of all three domains was
prokaryotic.
• It likely had a circular chromosome and structural
genes organized into operons.
• The three domains are products of billions of
years of natural selection. Prokaryotes were the
only life-forms for billions of years.
Figure 27.2 The Three Domains of the Living World
27 General Biology of the Prokaryotes
• Prokaryotes live all around and even within us.
• Prokaryotes are important to the biosphere:
Some perform key steps in the cycling of
nitrogen, sulfur, and carbon.
Some trap energy from the sun and from
inorganic chemical sources.
Some help animals digest their food.
27 General Biology of the Prokaryotes
• Prokaryotes are found in every conceivable
habitat on the planet.
They live at extremely hot temperatures.
They can survive extreme alkalinity and
saltiness.
Some survive in the presence of oxygen, while
others survive without it.
Some live at the bottom of the sea.
Some live in rocks more than 2 km into Earth’s
solid crust.
27 General Biology of the Prokaryotes
• Three shapes are common to prokaryotes:
spheres, rods, and curved or spiral forms.
• Spherical prokaryotes are called cocci (singular
coccus). Cocci live singly or in two- or three-
dimensional arrays of chains, plates, or blocks.
• Rod-shaped prokaryotes are called bacilli. These
live in chains or singularly.
• Chains (filaments) and other associations do not
signify multicellularity because each cell is viable
independently.
Figure 27.3 Shapes of Prokaryotic Cells
27 General Biology of the Prokaryotes
• The prokaryotic cell differs from the eukaryotic cell
in three important ways:
The DNA of the prokaryotic cell is not
organized within a membrane-enclosed
nucleus.
Prokaryotes have no membrane-enclosed
cytoplasmic organelles. Some do have plasma
membrane infoldings.
Prokaryotes lack a cytoskeleton and thus do
not divide by mitosis. Instead, they divide by
fission after replicating their DNA.
27 General Biology of the Prokaryotes
• Some prokaryotes are motile.
Some spiral bacteria called spirochetes use a
rolling motion made possible by modified
flagella called axial filaments.
Many cyanobacteria and some other bacteria
use a gliding mechanism.
Some aquatic prokaryotes move slowly up and
down in the water by adjusting the amount of
gas in gas vesicles.
The most common type of locomotion is driven
by flagella.
Figure 27.4 Structures Associated with Prokaryote Motility (Part 1)
Figure 27.4 Structures Associated with Prokaryote Motility (Part 2)
27 General Biology of the Prokaryotes
• Bacterial flagella consist of a single fibril made of
the protein flagellin projecting from the surface,
plus a hook and basal body.
• The structure of the bacterial flagellum is entirely
different from the eukaryotic flagellum.
• In addition, the prokaryotic flagellum rotates about
its base, rather than beating, as a eukaryotic
flagellum does.
Figure 27.5 Some Bacteria Use Flagella for Locomotion
27 General Biology of the Prokaryotes
• Most prokaryotes have a thick and stiff cell wall
containing peptidoglycan.
• Peptidoglycan is unique to bacteria.
• The Gram stain, developed by Hans Christian
Gram in 1884, separates bacteria into two distinct
groups based on the nature of their cell walls.
27 General Biology of the Prokaryotes
• In a Gram stain, cells are soaked in violet dye and
treated with iodine, then washed with alcohol and
counterstained with safranine.
• Gram-positive bacteria stain violet. Gram-negative
bacteria stain pink to red.
• Gram-positive cell walls have a thick layer of
peptidoglycan.
• Gram-negative cell walls have a second membrane
outside the cell wall, and the cell wall has less
peptidoglycan.
• The space between the outer membrane and the cell
wall is called the periplasmic space.
Figure 27.6 The Gram Stain and the Bacterial Cell Wall (Part 1)
Figure 27.6 The Gram Stain and the Bacterial Cell Wall (Part 2)
27 General Biology of the Prokaryotes
• Different features of the cell wall contribute to
disease-causing characteristics of some
prokaryotes.
• Many antibiotics act by disrupting cell-wall
synthesis and tend to have little or no effect on
eukaryotic cells.
27 General Biology of the Prokaryotes
• Prokaryotes reproduce asexually by fission.
• However, prokaryotes can exchange genetic
material through transformation, conjugation, and
transduction.
• Rates of division vary with species:
E. coli divides about once every 20 minutes.
The shortest known generation time for
prokaryotes is about 10 minutes.
Bacteria living deep in Earth’s crust might not
divide for as long as 100 years.
27 General Biology of the Prokaryotes
• The long evolutionary history of bacteria and
archaea has led to a diversity of metabolic
pathways.
• Obligate anaerobes live only in the absence of
oxygen. Oxygen is toxic to them.
• Facultative anaerobes can shift between
anaerobic metabolism (such as fermentation) and
the aerobic mode (cellular respiration).
• Aerotolerant anaerobes cannot conduct cellular
respiration, but are not damaged by oxygen when
it is present.
• Obligate aerobes are unable to survive for
extended periods in the absence of oxygen.
27 General Biology of the Prokaryotes
• There are four nutritional categories among
prokaryotes:
Photoautotrophs
Photoheterotrophs
Chemoautotrophs
Chemoheterotrophs
27 General Biology of the Prokaryotes
• Photoautotrophs are photosynthesizers, using light for
energy and CO2 as a carbon source
• Cyanobacteria use chlorophyll a and produce oxygen
as a byproduct.
• Other photosynthetic bacteria use bacteriochlorophyll
and do not produce O2. Some use H2S instead of H2O
as an electron donor and produce particles of pure
sulfur.
• Bacteriochlorophyll absorbs longer wavelengths than
other chlorophylls do. This longer wavelength of light
penetrates farther into water and is not absorbed by
plants.
Figure 27.7 Bacteriochlorophyll Absorbs Long-Wavelength Light
27 General Biology of the Prokaryotes
• Photoheterotrophs use light as a source of
energy but must get carbon from other organisms.
• They use carbohydrates, fatty acids, and alcohols
for carbon.
• Purple nonsulfur bacteria are photoheterotrophs.
27 General Biology of the Prokaryotes
• Chemolithotrophs obtain energy from oxidizing
inorganic substances and use some of the energy
to fix CO2.
• Some use pathways to fix CO2 identical to those
of the Calvin cycle.
• Others oxidize ammonia, hydrogen gas, hydrogen
sulfide, sulfur, or methane.
• Some deep-sea ecosystems around thermal
vents are based on chemolithotrophs, which form
the basis for a food chain that includes giant
worms, crabs, and mollusks.
27 General Biology of the Prokaryotes
• Chemoheterotrophs typically obtain energy and
carbon atoms from one or more organic
compounds.
• Most known bacteria and archaea are
chemoheterotrophs, as are all animals, fungi, and
many protists.
27 General Biology of the Prokaryotes
• Some bacteria use oxidized inorganic ions, such
as nitrate, nitrite, or sulfate, as electron acceptors.
• Denitrifiers are normally aerobic bacteria, mostly
Bacillus and Pseudomonas.
• Under anaerobic conditions they use NO3- in
place of oxygen as an electron acceptor.
• They release nitrogen to the atmosphere as N2
gas.
27 General Biology of the Prokaryotes
• Nitrogen fixers convert atmospheric N2 gas into
ammonia by means of the following reaction:
N2 + 6 H 2 NH3
• All organisms require fixed nitrogen for their
proteins, nucleic acids, and other nitrogen-
containing compounds.
• Only archaea and bacteria, including some
cyanobacteria, can fix nitrogen.
27 General Biology of the Prokaryotes
• Bacteria of two genera, Nitrosomonas and
Nitrosococcus, are nitrifiers, meaning that they
convert ammonia to nitrite.
• Nitrobacter is a nitrifier that oxidizes nitrite to
nitrate.
• Chemosynthesis in these bacteria is powered by
the energy released by the oxidation process.
27 Prokaryotes in Their Environments
• Prokaryotes are important in element cycling.
• Plants depend on prokaryotic nitrogen-fixers for
their nutrition.
• Denitrifiers prevent accumulation of toxic levels of
nitrogen in lakes and oceans.
• Cyanobacteria have had a powerful effect on
changing Earth by generating atmospheric O2.
• The accumulation of O2 in the atmosphere made
the evolution of more efficient glucose metabolism
possible and caused the extinction of many
species that couldn’t tolerate oxygen.
27 Prokaryotes in Their Environments
• Archaea help stave off global warming.
• There are ten trillion tons of methane lying deep
under the ocean floor.
• Archaea present at the bottom of the seas
metabolize this methane as it rises from its
deposits, preventing it from hastening global
warming.
27 Prokaryotes in Their Environments
• Prokaryotes live on and in other organisms:
Mitochondria and chloroplasts are assumed to be
descendants of free-living bacteria.
Plants and bacteria form cooperative nitrogen-
fixing nodules on the plant roots.
The tsetse fly obtains the vitamins needed for
reproduction from a bacterium living inside its
cells.
Cows depend on prokaryotes in their digestive
tract to digest cellulose.
Humans use vitamins B12 and K produced by our
intestinal bacteria.
27 Prokaryotes in Their Environments
• Koch’s postulates, or rules, for determining that a
particular microorganism causes a particular disease:
The microorganism must always be found in
individuals with the disease.
The microorganism can be taken from the host and
grown in pure culture.
A sample of the culture produces the disease
when injected into a new, healthy host.
The newly infected host yields a new, pure culture
of microorganisms.
27 Prokaryotes in Their Environments
• Only a tiny proportion of prokaryotic species are
pathogens. All known prokaryotic pathogens are
Bacteria (not Archaea).
• For an organism to be a pathogen, it must:
Arrive at the body surface.
Enter the body.
Evade detection and defenses.
Multiply inside the host.
Infect new hosts.
27 Prokaryotes in Their Environments
• For the host, the seriousness of the infection
depends on the invasiveness and the toxigenicity
of the pathogen.
• Corynebacterium diphtheriae, the agent that
causes diphtheria, has low invasiveness but
produces powerful toxins.
• Bacillus anthracis, which causes anthrax, has low
toxigenicity, but is so invasive that the
bloodstream of infected animals teems with
organisms.
27 Prokaryotes in Their Environments
• There are two major types of toxins:
Endotoxins, such those produced by
Salmonella and Escherichia are
lipopolysaccharides from the outer membrane
of Gram-negative bacteria. They are released
when the bacteria grow or lyse.
Exotoxins, which are produced and released
by living, multiplying bacteria, can be highly
toxic, even fatal.
• Tetanus, botulism, cholera, and plague are all
examples of exotoxins.
27 Prokaryotes in Their Environments
• Many unicellular microorganisms, prokaryotes in
particular, form dense films called biofilms.
• The cells lay down a gel-like polysaccharide matrix
when they contact a solid surface.This matrix traps
other bacteria, forming a biofilm.
• Biofilms can make bacteria difficult to kill. Pathogenic
bacteria may form a film that is impermeable to
antibiotics, for example.
• Biofilms can form on just about any available surface
and are the object of much current research.
27 Prokaryote Phylogeny and Diversity
• Classification schemes are used to help identify
unknown organisms, reveal evolutionary
relationships, and provide names for organisms.
• In the past, phenotypic characters such as color,
shape, antibiotic resistance, and staining were
used to classify prokaryotes.
• Now, nucleic acid sequencing is providing clues to
evolutionary relationships.
27 Prokaryote Phylogeny and Diversity
• Ribosomal RNA (rRNA) is particularly useful for
evolutionary studies for several reasons:
rRNA is evolutionarily ancient.
All organisms have rRNA.
rRNA functions the same way in all organisms.
rRNA changes slowly enough that sequence
similarities between groups of organisms are
easily found.
27 Prokaryote Phylogeny and Diversity
• Lateral gene transfer among bacteria of different
species has complicated the use of sequencing
information for determining the evolutionary
relationships of bacteria.
• There is currently great controversy over
prokaryotic phylogeny.
Figure 27.8 Two Domains: A Brief Overview
27 Prokaryote Phylogeny and Diversity
• Mutations are a major source of prokaryotic
variation.
• The rapid multiplication of many prokaryotes—
along with mutation, selection, and genetic drift—
causes rapid changes.
• Important changes, such as acquired resistance
to antibiotics, can occur broadly in just a few
years.
27 The Bacteria
• The most well-studied prokaryotes are the
bacteria.
• Focus will be on five groups: the proteobacteria,
cyanobacteria, spirochetes, chlamydias, and
firmicutes.
• Three of the bacterial groups that may have
branched out earliest are thermophiles.
27 The Bacteria
• The proteobacteria, or purple bacteria, make up
the largest group in terms of the number of
species.
• Some are Gram-negative, bacteriochlorophyll-
containing, and sulfur-using photoautotrophs.
However, others have dramatically different
phenotypes.
• The mitochondria of eukaryotes were derived
from proteobacteria by endosymbiosis.
27 The Bacteria
• The common ancestor to all proteobacteria was
probably a photoautotroph.
• Early in evolutionary history, two of the five
proteobacteria groups lost the ability to
photosynthesize and became chemoheterotrophs.
• There also are some chemolithotrophs and
chemoheterotrophs in all three of the other
groups.
• Some fix nitrogen (Rhizobium) and some help
cycle nitrogen and sulfur.
Figure 27.9 The Evolution of Metabolism in the Proteobacteria
27 The Bacteria
• Cyanobacteria (blue-green bacteria) are
photoautotrophs.
• They use chlorophyll a for photosynthesis and
release O2. Their photosynthesis was the basis of
the transformation of Earth’s atmosphere.
• Cyanobacteria have highly organized internal
membranes called photosynthetic lamellae or
thylakoids.
• Chloroplasts are derived from an endosymbiotic
cyanobacterium.
• Some filamentous colonies differentiate into three
cell types: vegetative cells, spores, and
heterocysts (specialized for nitrogen fixation).
Figure 27.11 Cyanobacteria (Part 1)
Figure 27.11 Cyanobacteria (Part 2)
27 The Bacteria
• Spirochetes are Gram-negative bacteria with
axial filaments, which are fibrils running through
the periplasmic space.
• The cell body is a long cylinder coiled into a spiral.
• Many spirochetes live in humans as parasites. A
few are pathogens (e.g., those that cause syphilis
and Lyme disease). Others live free in mud or
water.
Figure 27.12 A Spirochete
27 The Bacteria
• Chlamydias are Gram-negative intracellular
parasites that are among the smallest bacteria.
• Their life cycle involves two different forms of
cells: elementary bodies and reticulate bodies.
• In humans, they cause eye infections, sexually
transmitted disease, and some forms of
pneumonia.
Figure 27.13 Chlamydias Change Form during Their Life Cycle
27 The Bacteria
• Most firmicutes are Gram-positive, but some are
Gram-negative, and some have no cell wall at all.
• When a key nutrient becomes scarce, some produce
endospores, which are heat-resistant resting
structures.
The bacterium replicates its DNA and encapsulates
one copy in a tough cell wall, thickened with
peptidoglycan and covered with a spore coat.
The parent cell then breaks down, releasing the
endospore.
Some endospores can be reactivated after more
than a thousand years of dormancy.
Figure 27.14 The Endospore: A Structure for Waiting Out Bad Times
Figure 27.15 Gram-Positive Firmicutes
27 The Bacteria
• Actinomycetes are firmicutes that develop an
elaborately branched system of filaments.
• Some reproduce by forming chains of spores at
the tips of filaments.
• In others, the filamentous growth ceases and the
structure breaks up into typical cocci or bacilli,
which then reproduce by fission.
• Mycobacterium tuberculosis is an actinomycete.
• Most of our antibiotics are derived from
actinomycetes. Streptomyces produces the
antibiotic streptomycin, as well as hundreds of
other antibiotics.
Figure 27.16 Filaments of an Actinomycetes
27 The Bacteria
• Mycoplasmas lack cell walls, are the smallest
bacteria (some have a diameter of 0.2 µm), and
have the least amount of DNA.
• They may have the minimum amount of DNA
necessary to code for the essential properties of a
living cell.
Figure 27.17 The Tiniest Living Cells
27 The Archaea
• The study of Archaea is still in its very early stages.
• It is possible that the domain Archaea is
paraphyletic.
• Most archaea live in environments that are extreme
in one way or another: temperature, salinity,
oxygen concentration, or pH.
• There are two groups of Archaea: Euryarchaeota
and Crenarchaeota.
27 The Archaea
• The Archaea lack peptidoglycan in their cell walls
and have distinctive lipids in their cell membranes.
• When biologists sequenced the first archaean
genome, more than half of its 1,738 genes were
unlike any found in the other two domains.
• The unusual lipids in the membranes of archaea
are long fatty acids bonded to glycerol via an
ether linkage, as opposed to the ester linkage
found in other organisms.
Figure 27.18 Membrane Architecture in Archaea
27 The Archaea
• Most Crenarchaeota are both thermophilic and
acidophilic.
• Members of the genus Sulfolobus live in hot
sulfur springs at temperatures of 70–75ºC and
die at 55º C (131ºF).
• They grow best at pH 2–pH 3 but can survive
pH 0.9.
Figure 27.19 Some Would Call It Hell; Archaea Call It Home
27 The Archaea
• Some species of Euryarchaeota are
methanogens, producing methane (CH4) from
CO2.
• All methanogens are obligate anaerobes.
• Methanogens release approximately 2 billion tons
of methane gas into Earth’s atmosphere. About
one-third of this comes from methanogens in the
guts of grazing herbivores.
• Methanopyrus lives on the ocean bottom near
volcanic vents and can live at 110ºC.
27 The Archaea
• Some Euryarchaeota, called extreme halophiles,
live exclusively in very salty environments such as
the Dead Sea or in pickle brine.
• Some of these organisms survive a pH of 11.5.
• Some of the extreme halophiles use the pigment
retinol combined with a protein to form the light-
absorbing molecule bacteriorhodopsin, and make
ATP using a chemiosmotic mechanism.
Figure 27.20 Extreme Halophiles
27 The Archaea
• Thermoplasma is thermophilic and acidophilic; it
has no cell wall, an aerobic metabolism, and lives
in coal deposits.
• It has the smallest genome (1,100,000 base pairs)
of the archaea.