Bacteria and Archaea: The Prokaryotic Domains

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Bacteria and ArchaeaThe Prokaryotic Domains
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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

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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.

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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.

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Figure 27.2 The Three Domains of the Living World
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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.

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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 Earths
  solid crust.

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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.

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Figure 27.3 Shapes of Prokaryotic Cells
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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.

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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.

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Figure 27.4 Structures Associated with
Prokaryote Motility (Part 1)
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Figure 27.4 Structures Associated with
Prokaryote Motility (Part 2)
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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.

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Figure 27.5 Some Bacteria Use Flagella for
Locomotion
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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.

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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.

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Figure 27.6 The Gram Stain and the Bacterial
Cell Wall (Part 1)
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Figure 27.6 The Gram Stain and the Bacterial
Cell Wall (Part 2)
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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.

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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 Earths crust might not
  divide for as long as 100 years.

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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.

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General Biology of the Prokaryotes

• There are four nutritional categories among
  prokaryotes
• Photoautotrophs
• Photoheterotrophs
• Chemoautotrophs
• Chemoheterotrophs

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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.

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Figure 27.7 Bacteriochlorophyll Absorbs
Long-Wavelength Light
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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.

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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.

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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.

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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.

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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.

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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.

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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 couldnt tolerate oxygen.

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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.

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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.

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Prokaryotes in Their Environments

• Kochs 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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Figure 27.8 Two Domains A Brief Overview
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Prokaryote Phylogeny and Diversity

• Mutations are a major source of prokaryotic
  variation.
• The rapid multiplication of many
  prokaryotesalong with mutation, selection, and
  genetic driftcauses rapid changes.
• Important changes, such as acquired resistance to
  antibiotics, can occur broadly in just a few
  years.

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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.

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The Bacteria

• The proteobacteria, or purple bacteria, make up
  the largest group in terms of the number of
  species.
• Some are Gram-negative, bacteriochlorophyll-contai
  ning, and sulfur-using photoautotrophs. However,
  others have dramatically different phenotypes.
• The mitochondria of eukaryotes were derived from
  proteobacteria by endosymbiosis.

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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.

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Figure 27.9 The Evolution of Metabolism in the
Proteobacteria
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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 Earths 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).

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Figure 27.11 Cyanobacteria (Part 1)
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Figure 27.11 Cyanobacteria (Part 2)
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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.

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Figure 27.12 A Spirochete
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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.

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Figure 27.13 Chlamydias Change Form during Their
Life Cycle
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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.

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Figure 27.14 The Endospore A Structure for
Waiting Out Bad Times
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Figure 27.15 Gram-Positive Firmicutes
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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.

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Figure 27.16 Filaments of an Actinomycetes
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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.

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Figure 27.17 The Tiniest Living Cells
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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.

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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.

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Figure 27.18 Membrane Architecture in Archaea
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The Archaea

• Most Crenarchaeota are both thermophilic and
  acidophilic.
• Members of the genus Sulfolobus live in hot
  sulfur springs at temperatures of 7075ºC and die
  at 55º C (131ºF).
• They grow best at pH 2pH 3 but can survive pH
  0.9.

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Figure 27.19 Some Would Call It Hell Archaea
Call It Home
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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 Earths 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.

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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.

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Figure 27.20 Extreme Halophiles
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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.