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Transcript
Chapter 19:
Archaeal Diversity
1
Chapter Overview
Archaeal traits
● Crenarchaeota: Hyperthermophiles,
Mesophiles, and psychrophiles
● Euryarchaeota: Methanogens, Halophiles,
Thermophiles, and acidophiles
● Deeply branching divisions
●
2
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.
3
Secret lives of archaea, tools to search for extraterrestrial life
4
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
5
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
6
7
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
8
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
9
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
10
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
11
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
12
RNA polymerases in Archaea
behave more like those of
Eukarya
Transcription
factor B (TFB)
13
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,
14
alkalinophiles
Figure 19.5
15
Crenarchaeota
The name Crenarchaeota means “scalloped
archaea.”
- Are often irregular in shape
All crenarchaeotes synthesize a distinctive
tetraether lipid, called crenarchaeol.
Figure 19.6
16
Table 19-3 Hyperthermophilic Crenarchaeota.
17
Crenarchaeota
Desulfurococcales
- Lack cell walls, but have elaborate S-layer
- Reduce sulfur at higher temperatures
Desulforococcus mobilis
- Hot springs
Ignicoccus islandicus
- Marine organism
18
Hyperthermophiles:
Desulfurococcales: Reduce sulfur
from hot springs
D. mobilis
I. islandicus
Organic-C + S0  H2S + CO2 + H2O
H2 + S0  H2S
19
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
20
Pyrodictium abyssi: cells linked by cannulae
an example of single sp biofilm
21
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
22
Crenarchaeota
Sulfolobus
- No cell walls – only an S-layer of
glycoprotein
- Membrane composed mainly of
tetraethers with cyclopentane rings
Sulfolobus sp.
23
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
24
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.
25
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.
26
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
27
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.
28
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
29
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
30
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
31
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
32
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
33
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
34
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
35
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.
36
Figure 19.31
37
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
38
Figure 19.34
39
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
40
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
41
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
42
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
43
●
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
●
44
Pop Quiz
Which of the following is unique to Archaea?
a) S-layers
b) Supercoiled DNA
c) Thermophiles
d) Pseudopeptidoglycan
45