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Ch 29 Introduction
• Bacteria and Archaea form two of the three largest branches on the tree of life.
The third major branch or domain is Eukarya, the eukaryotes.
• Virtually all members of the bacteria and archaea are unicellular and all are
prokaryotic (lacking a membrane-bound nucleus).
• Bacteria and archaea are distinguished by the types of molecules that make up
their plasma membranes and cell walls, and by the machinery they use to
transcribe DNA and translate mRNA into proteins.
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The Biological Impact of Bacteria and Archaea
•
The oldest fossils found thus far are of 3.5-billion-year-old
bacteria. Eukaryotes do not appear in the fossil record until 1.7
billion years later.
• Only 5000 species of bacteria and archaea have been named and
described, but biologists are virtually certain that millions exist.
– Over 400 species live in the human digestive tract.
– About 128 species live in the lining of the human stomach.
– Approximately 500 species live in the human mouth.
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The Abundance of Prokaryotes
• About 1013 cells make up your body, but living on it are about 1012
bacterial cells on your skin, and about 1014 bacterial and archaeal
cells in your digestive tract.
• A teaspoon of soil contains billions of microbes.
• Current estimates place the number of living prokaryotes at over
5 x 1030—lined end-to-end they would stretch longer than the
Milky Way!
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The Habitat Diversity of Prokaryotes
• Bacteria and archaea live almost everywhere, from below the
Earth’s surface to on Antarctic sea ice.
– 10 percent of the world’s biomass may be comprised of
prokaryotes living under the ocean.
– Bacteria and archaea have been found at depths of 10,000 m,
and in temperatures ranging from 0° to 121°C.
• Entirely new phyla of bacteria and archaea have been recently
discovered.
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Medical Importance
• The first human disease-causing archaean, associated with the
dental condition called periodontitis, was just discovered in 2004.
• Bacteria that cause disease are said to be pathogenic.
– Only a tiny fraction of the bacterial species living on and in the
human body is pathogenic.
• Pathogenic bacteria tend to affect tissues at the body’s entry points,
such as wounds or pores in the skin, the respiratory and
gastrointestinal tracts, and the urogenital canal.
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Some Bacteria Cause Disease
• An infectious disease is one spread by being passed from an
infected individual to an uninfected individual.
• The experiments of Robert Koch in the late 1800s became the basis
for the germ theory of disease, which holds that infectious
diseases are caused by bacteria and viruses (acellular particles that
parasitize cells).
– Koch’s postulates confirm a causative link between a specific
infectious disease and a specific microbe:
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Koch’s Postulates
1. The microbe must be present in individuals suffering from the
disease and absent from healthy individuals.
2. The organism must be isolated and grown in a pure culture
away from the host organism.
3. If organisms from the pure culture are injected into a healthy
experimental animal, the disease symptoms should appear.
4. The organism should be isolated from the diseased
experimental animal, again grown in pure culture, and
demonstrated to be the same as the original organism.
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What Makes Some Bacterial Cells Pathogenic?
• Virulence, or the ability to cause disease, is heritable
• Some species have both pathogenic virulent strains and harmless
strains.
– In Escherichia coli, for example, the virulence of the strain
depends upon the length of the genome and the toxicity of the
resulting proteins.
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The Past, Present, and Future of Antibiotics
• The discovery of antibiotics (molecules that kill bacteria) in 1928
and their widespread use starting in the 1940s allowed physicians to
effectively combat most bacterial infections.
– (NOT viral infections)
• However, overuse of antibiotics since the late twentieth century has
lead to antibiotic-resistant strains of bacteria.
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Bacteria’s Role in Bioremediation
• Some of the most serious pollutants in soils, rivers, and ponds
consist of organic solvents or fuels that leaked or were spilled into
the environment.
• These pollutants are toxic, do not dissolve in water, and accumulate
in sediments.
• Bioremediation is the use of bacteria and archaea to degrade
pollutants.
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Bacteria’s Role in Bioremediation
• Bioremediation uses two complementary strategies:
1. Fertilizing contaminated sites to encourage the growth of
existing bacteria and archaea that degrade toxic compounds.
2. “Seeding,” or adding, specific species of bacteria and archaea
to contaminated sites.
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Extremophiles
• Bacteria or archaea that live in high-salt, high-temperature, lowtemperature, or high-pressure habitats are called extremophiles.
• Extremophiles have become a hot area of research for several
reasons:
1. Understanding extremophiles may help explain how life on
Earth began.
2. Astrobiologists use extremophiles as model organisms in
the search for extraterrestrial life.
3. Enzymes that function at extreme temperatures and pressures
are useful in industrial processes, such as the use of Taq
polymerase in PCR.
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Evaluating Molecular Phylogenies
• The universal tree illustrates that earlier phylogenetic trees based on
morphology, which showed the major division as between
prokaryotes and eukaryotes, were incorrect.
• The tree of life based on ribosomal RNA sequences shows the three
domains—Archaea, Bacteria, and Eukarya—that are now accepted
as correct.
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Morphological Diversity
• Bacteria and archaea show extensive morphological diversity in
terms of size, shape, and motility.
– The volume of bacterial species ranges from 0.15 m3 to
200 x 106 m3.
– Bacteria range in shape from filaments, spheres, rods, and
chains to spirals.
– Bacteria have a range of modes of motility.
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Metabolic Diversity: Bacteria/Archaea can eat ANYTHING!
•
Bacteria and archaea may use one of three sources of energy for
ATP production: light, organic molecules, or inorganic molecules.
– Phototrophs use light energy to promote electrons to the top of
electron transport chains. ATP is then produced by
photophosphorylation.
– Chemoorganotrophs oxidize organic molecules with high
potential energy. ATP may be produced by cellular respiration
using sugars as electron donors or by fermentation pathways.
– Chemolithotrophs oxidize inorganic molecules with high
potential energy. ATP is produced by cellular respiration with
inorganic compounds serving as the electron donor.
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Metabolic Diversity
• Bacteria and archaea may obtain building-block compounds in one of two ways,
by synthesizing them from simple starting materials or by absorbing them from
their environment.
– Autotrophs manufacture their own carbon-containing compounds.
– Heterotrophs live by consuming them.
• Of the six possible ways of producing ATP and obtaining carbon, just two are
observed among eukaryotes. But bacteria and archaea do them all.
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Prokaryotic Metabolism
• The basic chemistry required for photosynthesis, cellular
respiration, and fermentation originated in these lineages. Then the
evolution of variations on each of these processes allowed
prokaryotes to diversify into millions of species that occupy diverse
habitats.
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Producing ATP via Cellular Respiration
• Bacteria and archaea can exploit a wide variety of electron donors
and acceptors to accomplish cellular respiration.
• When electron donors other than sugars and electron acceptors
other than oxygen are used, by-products other than water and
carbon dioxide are produced.
• The metabolic diversity of bacteria and archaea explains:
– their ecological diversity.
– their key role in cleaning up some types of pollution.
– their role in global change, including nutrient cycling.
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Producing ATP via Fermentation
• Fermentation is a strategy for making ATP without using electron
transport chains. However, fermentation is much less efficient than
cellular respiration.
• The diversity of enzymatic pathways in bacterial and archaeal
fermentations extends the metabolic repertoire of these organisms.
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Producing ATP via Photosynthesis
• Photosynthetic species use the energy in light to raise electrons to
high-energy states.
– As these electrons are stepped down in energy through electron
transport chains, the energy released is used to generate ATP.
• Species that use water as a source of electrons carry out oxygenic
photosynthesis. Many phototrophic bacteria use molecules other
than water as the electron donor in anoxygenic photosynthesis.
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Obtaining Building-Block Compounds
• Many prokaryotes obtain building-block compounds in ways that
are quite different from eukaryotes:
– Several groups of bacteria fix CO2 using pathways other than
the Calvin cycle.
– Methanotrophs use methane (CH4) rather than CO2 as their
carbon source. Other bacteria can use carbon monoxide (CO)
or methanol (CH3OH) as a starting material.
– Compared to eukaryotes, the metabolic capabilities of bacteria
and archaea are remarkably sophisticated and complex.
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Ecological Diversity and Global Change
• Bacteria and archaea can live in extreme environments and use
toxic compounds as food because they produce extremely
sophisticated enzymes.
• The complex chemistry and abundance of bacteria and archaea
make them potent forces for global change.
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The Oxygen Revolution
• No free molecular oxygen existed for the first 2.3 billion years of Earth's history.
• Cyanobacteria, a lineage of photosynthetic bacteria, were the first organisms to
perform oxygenic (oxygen-producing) photosynthesis.
• Cyanobacteria were responsible for changing the Earth’s atmosphere to one with
a high concentration of oxygen.
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The Oxygen Revolution
• Once oxygen was common in the oceans, cells could carry out
aerobic respiration.
• Prior to this, only anaerobic respiration was possible; cells had to
use compounds other than oxygen as the final electron acceptor in
the electron transport chain during cellular respiration.
.
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Nitrogen Fixation and the Nitrogen Cycle
• All organisms require nitrogen (N) to synthesize proteins and
nucleic acids.
• Although molecular nitrogen (N2) is abundant in the atmosphere,
most organisms cannot use it directly.
– Therefore, all eukaryotes and many bacteria and archaea must
obtain their N in a form such as ammonia (NH3) or nitrate
(NO3).
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The Nitrogen Cycle
• The only organisms capable of
converting molecular nitrogen to
ammonia, a process called
nitrogen fixation, are specific
bacteria.
– Certain species of aquatic
cyanobacteria can fix
nitrogen.
– On land, nitrogen-fixing
bacteria live in close
association with plants—often
taking up residence in root
structures called nodules.
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Nitrogen Cycling
• The nitrite (NO2) that some bacteria produce as a by-product of
respiration does not build up in the environment but rather is used
as an electron acceptor by other species and converted to molecular
nitrate (NO3), which in turn is converted to molecular nitrogen (N2)
by yet another suite of bacterial and archaeal species.
• In this way, bacteria and archaea are responsible for driving the
movement of nitrogen atoms through ecosystems around the globe.
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Nitrate Pollution
• The widespread use of ammonia fertilizers
is causing serious pollution.
– When ammonia is added to the soil,
much of it is used by bacteria as food,
which then release nitrite (NO2–) or
nitrate (NO3–).
• Nitrates cause pollution in aquatic
environments.
– In an aquatic ecosystem, nitrates can
decrease the oxygen content, causing
anaerobic “dead zones” to develop.
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Summary of Prokaryotic Diversity
Bacteria and Archaea may be small in size, but because of their
abundance, ubiquity, and ability to do sophisticated chemistry,
they have an enormous influence on the global environment.
Gulf of
Mexico
dead zone
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Key Lineages of Bacteria and Archaea
• The relationships among the major lineages within Bacteria and
Archaea are still uncertain in some cases.
– However, most of the lineages themselves are well studied.
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Bacteria
• Bacteria are a monophyletic group. Within this group there are at
least 16 major lineages.
• Some were recognized by distinctive morphological characteristics,
others by phylogenetic analyses of gene sequence data.
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Bacteria
• Firmicutes are Gram positives and most are rod
shaped or spherical.
– They are metabolically diverse.
– Species in this group are important
components of soil.
– Some species in this group cause diseases,
yet we use some to ferment milk into
yogurt.
• Spirochaeles (spirochetes) are distinguished by
their corkscrew shape and unusual flagella.
– Most spirochetes produce ATP via
fermentation.
– These bacteria are very common in aquatic
habitats.
– Spirochetes cause the diseases syphilis and
Lyme disease.
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Bacteria
• Actinobacteria are Gram positive, and shape varies from rods to filaments.
– Many of the soil-dwelling species are found as chains of cells that form
extensive branching filaments called mycelia.
– Many species are heterotrophs. Some species live as decomposers in soil;
some live in association with plant roots and fix nitrogen.
– Tuberculosis and leprosy are caused by members of this group.
– Species from the genus Streptomyces produce over 500 distinct antibiotics.
Mycelia
Mycobacterium leprae
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Bacteria
• Chlamydiae are spherical and
very tiny.
– They are endosymbionts—
they live as parasites inside
animal cells and get almost
all of their nutrition from
their hosts.
– These bacteria can cause
blindness and urogenital tract
infections in humans.
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Bacteria
• Cyanobacteria were formerly known as “blue-green algae.” They
are found as independent cells, chains, or colonies.
– All perform oxygenic photosynthesis; they produce oxygen,
nitrogen, and organic compounds that feed other organisms in
aquatic environments.
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Bacteria
• Proteobacteria form five major subgroups and are very diverse in
morphology and metabolism.
– Some proteobacteria can form colonies, which can produce a
structure called a fruiting body.
– Pathogenic proteobacteria cause Legionnaire’s disease, cholera,
dysentery, and gonorrhea.
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Archaea
• Archaea live in virtually every habitat, including extreme
environments.
– However, there are no known parasitic archaea.
• Domain Archaea is composed of at least two major lineages.
• The domain was discovered so recently that major groups are still
being discovered and described.
– Two additional lineages may exist.
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Archaea
• Crenarchaeota can be shaped like filaments, rods, discs, or
spheres.
– They are metabolically diverse, although some make ATP only
through fermentation.
– They are the only life-forms present in certain extreme
environments, such as high-pressure, very hot, cold, or acidic
environments.
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Archaea
• The Euryarchaeota come in many shapes.
– They live in every conceivable habitat, including high-salt,
high-pH, and low-pH environments.
– They include the methanogens, which contribute about 2
billion tons of methane to the atmosphere each year.
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