Chapter 19:
Archaeal Diversity
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Chapter Overview
Archaeal traits
● Crenarchaeota: Hyperthermophiles,
Mesophiles, and psychrophiles
● Euryarchaeota: Methanogens, Halophiles,
Thermophiles, and acidophiles
● Deeply branching divisions
●
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Introduction
Archaea are the most ecologically diverse of the
three domains.
- Psychrophiles
- Hyperthermophiles
- Halophiles
- Acidophiles
- Methanogens
Archaea are also abundant in moderate habitats.
- Open ocean, soil, and surface of plant roots
Surprisingly, the archaeal domain lacks pathogens.
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Secret lives of archaea, tools to search for extraterrestrial life
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Archaeal Traits
The Archaea have unique key features, as
well as traits shared by other domains.
Distinctive features of archaea, sometimes
called “archaeal signatures,” include:
- Cell membrane lipids
- Cell wall components
- Certain metabolic pathways
- Certain genome features
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Archaeal Lipids
Are different from those of bacteria and eukaryotes
- Use L-glycerol, not D-glycerol
- Have ether (R–O–R) not ester (R–COO–R) links
- Are branched chains of lipids
- Made from isoprenoid units
- No unsaturations in lipids
- Can be more exotic in form
- Macrocyclic diether
- Tetraether – makes a single layer
- Cyclopentane rings
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Archaeal Cell Walls and Other
Characteristics
Archaea show distinctive versions of the cell wall.
- Pseudopeptidoglycan in methanogens
- N-acetyltalosaminuronic acid
- b(1,3) linkages instead of b(1,4)
- Are therefore resistant to lysozyme
- Different types of cross-bridges
- Are therefore resistant to penicillin
- Other Archaea possess no cell wall at all.
- Only an S-layer composed of protein
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Chromosome - single (closed circular) molecule of doublestranded DNA (one-third to one-half as much DNA per cell as
found in bacteria such as E. coli)
Plasmids - these pieces of extrachromosomal DNA may make
up as much as 25-30% of cellular DNA
Endospores - not formed
Flagella- very long protein (flagellin) polymers that provide
motility
Pili- long thin protein polymers that act as cell "anchors" to
various surfaces and can assist in attaching archaeal cells to
facilitate DNA transfer from
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Archaeal Metabolic Pathways
Glucose is catabolized by
several variants of the
Entner-Doudoroff (ED)
and Embden-MeyerhoffParnas (EMP) pathways
that rarely occur in
bacteria.
The process of
methanogenesis is
unique to Archaea.
Figure 19.3
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Archaeal Genomes
Unique features of Archaea
- “Reverse gyrase” of hyperthermophiles
- Maintains positive supercoils
Similarities to bacteria
- Circular genome
- Gene size and density
- Presence of operons (what is an operon?)
Similarities to eukaryotes
- Presence of introns (what are introns?)
- RNA polymerase has TBP and TFIIB
- Presence of histone homologs
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An intron is any nucleotide sequence within a gene that
is removed by RNA splicing to generate the final mature
RNA product of a gene
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RNA polymerases in Archaea
behave more like those of
Eukarya
Transcription
factor B (TFB)
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Phylogeny of Archaea
The domain Archaea includes two phyla:
- Crenarchaeota
- Shows a wider range of temperature
diversity
- Hyperthermophiles, thermophiles,
mesophiles, and psychrophiles
- Euryarchaeota
- Shows a greater range of metabolism
- Methanogens, halophiles, acidophiles,
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alkalinophiles
Figure 19.5
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Crenarchaeota
The name Crenarchaeota means “scalloped
archaea.”
- Are often irregular in shape
All crenarchaeotes synthesize a distinctive
tetraether lipid, called crenarchaeol.
Figure 19.6
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Table 19-3 Hyperthermophilic Crenarchaeota.
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Crenarchaeota
Desulfurococcales
- Lack cell walls, but have elaborate S-layer
- Reduce sulfur at higher temperatures
Desulforococcus mobilis
- Hot springs
Ignicoccus islandicus
- Marine organism
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Hyperthermophiles:
Desulfurococcales: Reduce sulfur
from hot springs
D. mobilis
I. islandicus
Organic-C + S0  H2S + CO2 + H2O
H2 + S0  H2S
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Crenarchaeota
Barophilic
hyperthermophiles
- Grow near
hydrothermal vents on
the ocean floor
- A common feature is
the black smoker.
- Crenarchaeotes that are
vent-adapted:
- Pyrodictium abyssi
- Pyrodictium occultum
-Pyrodictium brockii
•Grow at 100 –1200 C
•Reduce sulfur to H2S
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Pyrodictium abyssi: cells linked by cannulae
an example of single sp biofilm
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Crenarchaeota
Sulfolobales (terrestrial sulfur-contaning
hot springs
- Include species that respire by oxidizing
sulfur (instead of reducing it)
- Sulfolobus solfataricus
- A “double extremophile”
- Grows at 80oC and pH 3
- Oxidizes H2S to sulfuric acid
H2S + 3O2 + 2H2O  2H2SO4
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Crenarchaeota
Sulfolobus
- No cell walls – only an S-layer of
glycoprotein
- Membrane composed mainly of
tetraethers with cyclopentane rings
Sulfolobus sp.
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Other Thermophilic
Crenarchaeotes
Caldisphaerales
- Anaerobes and microaerophiles
- Respire anaerobically or ferment
- Grow up to 80oC at pH 3
Thermoproteales
- Include some of the smallest cells
- Reduce sulfur with H2 to H2S
- Grow up to 97oC at pH < 3
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Crenarchaeota
Also include mesophiles and psychrophiles
- Grow throughout the ocean
- Abundance varies according to season and
increases with depth.
- These uncultivated organisms are likely the
predominant crenarchaeotes on Earth.
Psychrophilic species also grow in sea ice off
Antarctica and in the marine benthos, or seafloor,
sediment.
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Crenarchaeota
The crenarchaeote
Cenarchaeum
symbiosum inhabits
the sponge Axinella
mexicana.
- The relationship is
unclear, but they can
be co-cultured in an
aquarium for many
years.
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Euryarchaeota: Methanogens
Euryarchaeota means “broad-ranging archaea.”
Are dominated by methanogens
- All are poisoned by molecular oxygen and
therefore require complete anaerobiosis.
- Major substrates and reactions include:
Carbon dioxide: CO2 + 4H2 → CH4 + 2H2O
Acetic acid: CH3COOH → CH4 + CO2
Methanol: 4CH3OH → 3CH4 + CO2 + 2H2O
Methylamine: 4CH3NH2 + 2H2O →
3CH4 + CO2 + 4NH3
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The methanogens include four classes.
- Thermophiles and mesophiles are found in all.
They display an astonishing diversity of cell forms.
- Rods (single or filamentous), cocci, and spirals
Figure 19.20
The methanogens have rigid cell walls made up of
pseudopeptidoglycan, proteins, or sulfated sugars.
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Filamentous methanogens form chains of large cells.
- Methanosaeta performs key functions in the
treatment of sewage waste.
- Traps bacteria into residual sludge
Figure 19.21
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Anaerobic Habitats for Methanogens
Methanogens grow in:
- Anaerobic soil of wetlands
- Especially rice paddies
- Landfills
- Digestive tracts of animals
- Termites
- Cattle
- Humans
- Marine benthic sediments
Figure 19.22A
Figure 19.22B
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Biochemistry of Methanogenesis
Biochemical pathways
of methanogens
involve unique
cofactors.
- These transfer the
hydrogens and
increasingly reduced
carbon to each
enzyme in the
pathway.
Figure 19.25
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Biochemistry of Methanogenesis
The process fixes CO2
onto the cofactor
methanofuran (MFR).
- The carbon is then
passed stepwise from
one cofactor to the
next, each time losing
an oxygen to form
water, or gaining a
hydrogen carried by
another cofactor.
Figure 19.26
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Euryarchaeota: Halophiles
Main inhabitants of high-salt environments are
members of the class Haloarchaea.
Figure 19.28
- Their photopigments color
salterns, which are used for
salt production.
- Most are colored red by
bacterioruberin, which
protects them from light.
Halophilic archaea require at
least 1.5M NaCl.
Figure 19.29B
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Haloarchaea adapt to high external NaCl by
maintaining high intracellular KCl .
- This requires major physiological adaptations,
such as high-GC-content DNA and acidic proteins.
Haloarchaea are generally mesophilic.
- Can be neutralophilic or alkalinophilic
Haloarchaea display considerable diversity in shape.
Figure 19.30
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Habitats for Haloarchaea
Different kinds of hypersaline habitats support
different species of haloarchaea.
- Thalassic lakes
- Athalassic lakes
- Solar salterns
- Brine pools beneath the ocean
- Alkaline soda lakes
- Antarctic brine lakes
- Underground salt deposits
- Salted foods
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Retinal-Based Photoheterotrophy
Most haloarchaea are photoheterotrophs.
Rhodopsins capture light energy.
- Bacteriorhodopsin (BR) pumps out H+.
- Halorhodopsin (HL) pumps in Cl–.
- Both increase proton motive force.
- Use proton gradient to pump out Na+
- Other rhodopsins signal to the flagellum.
- Phototaxis
- Flagellum uses Na+ to rotate.
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Figure 19.31
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Euryarchaeota: Thermophiles
Thermococcales
Figure 19.33A
- Include Thermococcus and
Pyrococcus
- Most are anaerobes.
- Use sulfur as a terminal
electron acceptor
Archaeoglobus
- Archeoglobales fulgidus
- Reduces sulfate to sulfide
- Runs methanogenesis in
reverse
Figure 19.33B
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Figure 19.34
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Euryarchaeota: Acidophiles
Thermoplasmatales
- Include acidophiles (as well as thermophiles)
- Have no cell walls and no S-layers
- Thermoplasma acidophilum
- Metabolism is based on S0 respiration of
organic molecules.
- Ferroplasma species
- Oxidize sulfur to sulfuric acid
- Generate pH values below pH 0
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Nanoarchaeota
The smallest known euryarchaeotes.
Nanoarchaeum equitans
- Is an obligate symbiont
of the crenarchaeote
Ignicoccus hospitalis
- Host and symbiont
genomes have been
sequenced, revealing
extensive coevolution.
Figure 19.36
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Deeply Branching Divisions
New archaeal species continue to be
discovered through PCR-amplified rDNA
probes.
- Most such strains are uncultivated.
A deeply branching division is the Ancient
Archaeal Group (AAG) of
hyperthermophiles.
- Includes the Korarchaeota
- Korarchaeum cryptophilum, which
grows in long thin filaments
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Chapter Summary
Archaea is the most ecologically diverse domain.
● Distinctive features of archaea include: membrane
lipid structure, cell wall composition, and metabolic
pathways.
● The domain Archaea includes two major phyla:
- Crenarchaeota: Show a wider temperature range
- Euryarchaeota: Show a greater metabolism range
● Crenarchaeota thermophiles include:
- Desulforococcales: Anaerobes that reduce sulfur
- Sulfolobales: Aerobes that oxidize sulfur
- Caldisphaerales and Thermoproteales: Anaerobic
acidophiles
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●
Chapter Summary
Crenarchaeotes also include mesophiles and thermophiles,
as well as ammonia oxidizers.
● Methanogens dominate the Euryarchaeota.
- They inhabit anaerobic environments.
- They have rigid cells wall and come in diverse shapes.
- Biochemical pathways involve unique cofactors.
● Halophilic archaea belong to the Euryarchaeota.
- Show molecular adaptations to high salt
- Exhibit retinal-based photoheterotrophy
● Euryarchaeota include thermophiles and acidophiles.
- Thermococcales, Archaeoglobus, and Thermoplasmatales
● Nanoarchaeota are the smallest euryarchaeotes
●
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Pop Quiz
Which of the following is unique to Archaea?
a) S-layers
b) Supercoiled DNA
c) Thermophiles
d) Pseudopeptidoglycan
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