CHAPTER 13
Prokaryotic Diversity: The Archaea
PART I Phylogeny and General
Metabolism
Phylogenetic Overview of the
Archaea
• Archaea form four major phyla, the
Euryarchaeota, the Crenarchaeota, the
Korarchaeota, and the Nanoarchaeota.
• Figure 13.1 shows a phylogenetic tree of
Archaea.
Energy Conservation and
Autotrophy in Archaea
• With the exception of methanogenesis,
bioenergetics and intermediary metabolism in
species of Archaea are much the same as
those in various species of Bacteria.
• Several Archaea are chemoorganotrophic
and thus use organic compounds as energy
sources for growth. Chemolithotrophy is also
well established in the Archaea, with H2 being
a common electron donor.
• The capacity for autotrophy is widespread in
the Archaea and occurs by several different
pathways. In methanogens, and presumably in
most chemolithotrophic hyperthermophiles,
CO2 is incorporated via the acetyl-CoA
pathway or some modification thereof.
Phylum Euryarchaeota
Extremely Halophilic Archaea
• Extremely halophilic Archaea require large
amounts of NaCl for growth. These organisms
accumulate high levels of KCl in their
cytoplasm as a compatible solute.
• These salts affect cell wall stability and
enzyme activity. The light-mediated proton
pump bacteriorhodopsin helps extreme
halophiles make ATP (Figure 13.4).
Model for the mechanism of bacteriorhodopsin activity
Light near 570 nm converts the protonated retinal bacteriorhodopsin from the trans form (RetT)
to the cis form (RetC), along with translocation of a proton to the outer surface of the membrane,
thus establishing a proton motive force. ATPase activity is driven by proton motive force.
Chlorophyll pigments
also synthesize ATP, a
light driven process
• Table 13.1 gives the ionic composition of
some highly saline environments.
• Table 13.2 lists the currently recognized
species of extremely halophilic Archaea.
Methane-Producing Archaea:
Methanogens
• A large number of Euryarchaeota produce
methane (CH4) as an integral part of their
energy metabolism. Such organisms are
called methanogens. Methanogenic Archaea
are strictly anaerobic prokaryotes.
• Habitats of methanogenic Archaea are listed
in Table 13.4.
• Table 13.5 gives characteristics of some
methanogenic Archaea.
• Substrates converted to methane by various
methanogenic Archaea are listed in Table
13.6. Acetotrophic substrates are those that
consume acetate.
Thermoplasmatales:
Thermoplasma, Ferroplasma,
and Picrophilus
• Thermoplasma, Ferroplasma, and
Picrophilus are extremely acidophilic
thermophiles that form their own phylogenetic
family of Archaea inhabiting coal refuse piles
and highly acidic solfataras.
• Cells of Thermoplasma and Ferroplasma
lack cell walls and thus resemble the
mycoplasmas in this regard.
• To survive the osmotic stresses of life
without a cell wall and to withstand the dual
environmental extremes of low pH and high
temperature, Thermoplasma has evolved a
unique cell membrane structure (Figure
13.11).
Structure of the tetraether lipoglycan of Thermoplasms
acidophilum – monolayer of lipid rather than bilayer membrane
Hyperthermophilic
Euryarchaeota:
Thermococcales and
Methanopyrus
• A few euryarchaeotes thrive in thermal
environments, and some are
hyperthermophiles. All organisms in this
group have growth temperature optima above
80°C.
• Thermococcus is a spherical
hyperthermophilic euryarchaeote indigenous
to anoxic thermal waters in various locations
throughout the world.
• Methanopyrus is a rod-shaped
hyperthermophilic methanogen isolated from
sediments near submarine hydrothermal
vents and from the walls of "black smoker"
hydrothermal vent chimneys.
• Methanopyrus is unusual because it contains
membrane lipids found in no other known
organism.
•In the lipids of Archaea, the glycerol side
chains contain phytanyl rather than fatty
acids bonded in ether linkage to the glycerol.
• In Methanopyrus, this ether-linked lipid is an
unsaturated form of the otherwise saturated
dibiphytanyl tetraethers found in other
hyperthermophilic Archaea (Figure 13.13).
Methanopyrus produces CH4 from CO2 and H2
Unsaturated phytanyl, Geranylgeraniol produced by Methanopyrus for
cell membranes
Hyperthermophilic
Euryarchaeota: The
Archaeoglobales
• Archaeoglobus was isolated from hot marine
sediments near hydrothermal vents. In its
metabolism, Archaeoglobus couples the
oxidation of H2, lactate, pyruvate, glucose, or
complex organic compounds to the reduction
of sulfate to sulfide.
• Ferroglobus is related to Archaeoglobus but
is not a sulfate-reducing bacterium. Instead,
Ferroglobus is an iron-oxidizing
chemolithotrophic autotroph, conserving
energy from the oxidation of Fe2+ to Fe3+
coupled to the reduction of NO3– to NO2– plus
NO (see Table 13.8).
PART III Phylum
Crenarchaeota
Habitats and Energy
Metabolism of Crenarchaeotes
• Table 13.7 summarizes the habitats of
Crenarchaeota. They include very hot and
very cold environments.
• Most hyperthermophilic Archaea have been
isolated from geothermally heated soils or
waters containing elemental sulfur and
sulfides.
•Hyperthermophilic Crenarchaeota inhabit the
hottest habitats currently known to support
life.
• Cold-dwelling crenarchaeotes have been
identified from community sampling of
ribosomal RNA genes from many nonthermal
environments.
• Crenarchaeotes have been found in marine
waters worldwide and thrive even in frigid
waters and sea ice.
Hyperthermophiles from
Terrestrial Volcanic Habitats:
Sulfolobales and
Thermoproteales
• Two phylogenetically related organisms
isolated from these environments include
Sulfolobus and Acidianus. These genera form
the heart of an order called the Sulfolobales
(Table 13.9).
• Key genera within the Thermoproteales are
Thermoproteus, Thermofilum, and
Pyrobaculum.
Hyperthermophiles from
Submarine Volcanic Habitats:
Desulfurococcales
• Submarine volcanic habitats are homes to the most
thermophilic of all known Archaea. These habitats
include both shallow-water thermal springs and deepsea hydrothermal vents.
• Pyrodictium and Pyrolobus are examples of
prokaryotes whose growth temperature
optimum lies above 100ºC. The optimum for
Pyrodictium is 105ºC and for Pyrolobus is
106ºC.
• Cells of Pyrodictium are irregularly discshaped and grow in culture in a mycelium-like
layer attached to crystals of elemental sulfur.
• Other notable members of the
Desulfurococcales include Desulfurococcus
and Ignicoccus.
• Like Pyrodictium, Desulfurococcus is a
strictly anaerobic S0-reducing bacterium, but
it differs from Pyrodictium in that it is much
less thermophilic, growing optimally at about
85°C. Ignicoccus grows optimally at 90ºC,
and its metabolism is H2/S0 based.
Phylum Nanoarchaeota
Nanoarchaeum
• Nanoarchaeum is a small, parasitic, earlybranching member of the Archaea. Its genome
is the smallest of all known organisms.
Nanoarchaeum lacks genes for all but core
molecular processes and thus depends on its
host, Ignicoccus, for most of its cellular needs.
Evolution and Life at High
Temperatures
Heat Stability of Biomolecules
• Although hyperthermophiles live at very
high temperatures, in some cases above the
boiling point of water, there are temperature
limits beyond which no living organism can
survive. This limit is likely 140ºC to 150°C
(Figure 13.25).
• Protein and DNA stability in
hyperthermophiles is critical to surviving high
temperature. Because most proteins denature
at high temperatures, much research has been
done to identify the properties of thermostable
proteins.
• The solution to protein thermostability turns
on the folding of the molecule. Temperature is
also a factor, and unique solutions have
evolved in hyperthermophiles to keep their
DNA intact.
• Hyperthermophilic prokaryotes typically
produce special classes of chaperonins that
function only at the highest growth
temperatures.
•In cells of Pyrodictium, for example, the
major chaperonin is a protein complex called
the thermosome.
• This complex (thermosome) functions to
keep the cell's other proteins properly folded
and functional at high temperature and can
help cells survive even above their maximal
growth temperature.
• All hyperthermophiles produce a DNA
topoisomerase called reverse DNA gyrase.
•Reverse gyrase introduces positive supercoils
into DNA (in contrast to the negative
supercoils introduced by DNA gyrase, found
in all nonhyperthermophilic prokaryotes).
Hyperthermophilic Archaea,
H2, and Microbial Evolution
• Why do so many Archaea seem to inhabit
extreme environments?
•Extreme environments of various types
existed on early Earth just as they do today,
and it is within such environments that life
may first have flourished.
• At the time that cellular life evolved nearly 4
billion years ago, it is almost certain that
Earth was far hotter than it is today and
probably suitable only for hyperthermophiles.
• If life originated on a hot planet Earth, as
most evolutionary scenarios predict, then
hyperthermophilic Archaea and Bacteria are
likely the closest living relatives to early life
forms that remain today.
•Therefore the biology of these
hyperthermophiles is not only interesting but
may offer us a window into the past.
• Hydrogen catabolism may have been the
first energy-yielding metabolism of cells.