Download Archaea

20
The Archaea
1
Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display.
20.1 Overview of the Archaea
1. List some common habitats in which archaea reside
2. Describe the debate that surrounds archaeal
taxonomy
3. Compare at least three key metabolic pathways that
are central to archaeal physiology with those used by
bacteria
2
Archaea
• Many features in common with Eukarya (真核)
– genes encoding proteins for replication, transcription,
translation
• Features in common with Bacteria
– genes encoding proteins for metabolism
• Other elements are unique to Archaea
– unique rRNA gene structure
– capable of methanogenesis
• Highly diverse with respect to morphology, physiology,
reproduction, and ecology
• Best known for growth in anaerobic, hypersaline, pH
extremes, and high-temperature habitats
• Also found in marine arctic temperature and tropical
waters
3
Archaeal Taxonomy
• 5 major physiological and morphological groups
4
Archaeal Taxonomy
• Two phyla based on
Bergey’s Manual
– Euryarchaeota (寬廣古菌)
– Crenarchaeota (熱泉古菌)
• Metagenomic analysis
reveals additional species
(some are not culturable)
• 16S rRNA and SSU rRNA
analysis also shows
– Group I are Thaumarchaeota
(奇古菌)
– Group II are Korachaeota (初
古菌)
5
6
Archaeal Metabolism
• Great variation among the different archaeal
groups
• Organotrophy, autotrophy, and phototrophy have
been observed
• Differ from other groups in glucose catabolism,
pathways for CO2 fixation, and the ability of some to
synthesize methane (甲烷)
7
Archaeal Metabolism: Autotrophy
• Carbon fixation pathways include
– Reductive acetyl-CoA pathway
– 3-hydroxyproprionate/4-hydroxybutyrate (HP/HB) cycle
– Dicarboxylate/4-hydroxybutyrate (DC/HB) cycle
8
Archaeal Metabolism: Autotrophy-1
• Reductive acetyl-CoA pathway
– Most energy efficient (1 ATP burned/pyruvate formed)
– 2 CO2 molecules incorporated into 1 acetyl group
– Acetyl group combined with additional CO2 to form pyruvate
– Used by methanogens both for carbon fixation and for energy
conservation
9
Archaeal Metabolism: Autotrophy-2 & 3
– 5 ATP/pyruvate
formed
– Found in
anaerobic and
microaerobic
members
HP/HB cycle
DC/HB cycle
– Some of its
enzymes are
sensitive to
oxygen
– Steps are similar
to a reversal of
the TCA cycle
– 9 ATP/
pyruvate
synthesized
– Can be
operated
under aerobic
conditions
– Has less of a
demand for
metal
cofactors
10
Acetyl-CoA Assimilation: Glyoxylate
(red lines) and Methylaspartate
Pathways (black lines)
Autotrophic
archaea and some
haloarchaea use
the glyoxylate
pathway
Haloarchaea lack
ICL and use the
methylaspartate
pathway
11
Archaeal Metabolism
Chemoorganotropy-1:
modified EmbdenMeyerhof
• Similarities in eukaryotes
and bacteria
• 3 pathways unique to
Archaea
– modified Embden-Meyerhof
pathway
– 2 modified Entner-Duodoroff
pathways
12
Chemoorganotropy-2:
2 modified EntnerDuodoroff
pathways
13
20.2 Phylum Crenarchaeota
1. List the major physiological types among
crenarchaea
2. Evaluate the importance of crenarchaeol in the
discovery of new crenarchaeotes
3. Discuss hyperthermophilic and thermoacidophilic
growth
14
Phylum Crenarchaeota
• Most are extremely thermophilic
– hyperthermophiles (hydrothermal vents)
• Most are strict anaerobes
• Some are acidophiles
• Many are sulfur-dependent
– for some, used as electron acceptor in anaerobic
respiration
– for some, used as electron source
15
Parasitic
Nanoarchaeum
attaches to
Ignicoccus
Boiling
temperature
and rich in
sulfur
16
Hyperthermophilic Crenarchaeote
• Pyrodiciaceae is
hyperthermophilic as
it can survive
autoclaving for an hour
• Strictly anaerobic
• Use H2 as a electron
donor and Fe3+ as an
electron acceptor
17
Crenarchaeota…
• Include organotrophs and lithotrophs (sulfuroxidizing and hydrogen-oxidizing)
• Contains 25 genera
– two best studied are Sulfolobus and Thermoproteus
18
Genus Thermoproteus
• Long thin rod, bent or branched
– cell walls composed of glycoprotein
• Thermoacidophiles
– 70–97 °C
– pH 2.5–6.5
• Anaerobic metabolism
– lithotrophic on sulfur and hydrogen
– organotrophic on sugars, amino acids, alcohols, and organic acids
using elemental sulfur as electron acceptor
• Autotrophic using CO or CO2 as carbon source
19
Genus Sulfolobus
• Irregularly lobed, spherical shaped
– cell walls contain lipoproteins and carbohydrates
• Thermoacidophiles
– 70–80°C
– pH 2–3
• Metabolism
– lithotrophic on sulfur using oxygen (usually) or ferric iron as
electron acceptor
– organotrophic on sugars and amino acids
20
Genome Construction of Sulfolobus
21
Phylum Crenarchaeota
• Group I archaea
– archaeal unique membrane lipid, crenarchaeol is widespread in
nature
• marine waters
• rice paddies, soil, freshwater
• Recent growth of mesophilic archaea
– capable of nitrification (ammonia to nitrate)
22
20.3 Phylum Euryarchaeota
1. Outline the process of methanogenesis and discuss its
importance in the flow of carbon through the biosphere
as well as in the production of energy
2. Discuss the physiology and ecology of anaerobic methane
oxidation
3. Explain the strategies halophiles have evolved to cope
with osmotic stress and why these strategies are needed
4. Outline rhodopsin-based phototrophy as used by
halophiles
5. Describe the habitats in which methanogens and
halophiles reside
6. List one unique feature for Thermoplasma, Pyrococcus,
and Archaeoglobus
23
Phylum Euryarchaeota
• Consists of many classes, orders, and families
• Often divided informally into five major groups
1. methanogens
2. halobacteria
3. thermoplasms
4. extremely thermophilic S0-metabolizers
5. sulfate-reducers
24
1. Methanogens
• All methanogenic microbes are Archaea
– called methanogens: produce methane
• Methanogenesis
– last step in the degradation of organic compounds
– occurs in anaerobic environments
• e.g., animal rumens
• e.g., anaerobic sludge digesters
• e.g., within anaerobic protozoa
25
Methanogens
• 26 genera, largest group of cultured archaea
– differ in morphology
– 16S rRNA
– cell walls
– membrane lipids
26
27
Methanogens
• Unique anaerobic production of methane
– hydrogen, CO2 oxidation
– coenzymes, cofactors
– ATP production linked with methanogenesis
• What are the
potential
mechanisms by
which methanogens
are thought to
couple CO2 reduction
to ATP generation?
28
29
Ecological and Practical
Importance of Methanogens
• Important in wastewater treatment
• Can produce significant amounts of methane
– can be used as clean burning fuel and energy source
– is greenhouse gas and may contribute to global warming
• Can oxidize iron
– contributes significantly to corrosion of iron pipes
• Can form symbiotic relationships with certain bacteria,
assisting carbon/sulfur cycling
30
2. Halobacteria
• Order Halobacteriales; 17 genera in one family,
Halobacteriaceae
• Extreme halophiles (halobacteria)
– require at least 1.5 M NaCl
• cell wall disintegrates if [NaCl] < 1.5 M
– growth optima near 3–4 M NaCl
• Aerobic, respiratory, chemoheterotrophs with
complex nutritional requirements
31
Strategies to Cope with Osmotic Stress
• Increase cytoplasmic osmolarity
– use compatible solutes (small organics)
• “Salt-in” approach
– use Na+/H+ antiporters/K+ symporters to increase concentration
of KCl and NaCl to level of external environment
• Acidic amino acids in proteins
– Acidic aa on the surface of the folded protein attract cations, which
form a hydrated shell on the protein
32
e.g., Halobacterium salinarium (H.
halobium)
• Has unique type of photosynthesis
– not chlorophyll based
– uses modified cell membrane (contains bacteriorhodopsin)
– absorption of light by bacteriorhodopsin drives proton
transport, creating PMF for ATP synthesis
33
Features of Halobacterium
Rhodopsins
• Bacteriorhodopsin: light-driven ion pumps
– chromophore similar to retinal
– seven membrane spanning domains
– purple aggregates in membrane
• Halorhodopsin: light-driven ion pumps
– light energy to transport chloride ions
• 2 sensory rhodopsins: photosensory receptors
– flagellar attached photoreceptors
34
Genomic Reconstruction of of
Halobacterium NRC-1
35
Proteorhodopsin
• Now known to be widely distributed among
bacteria and archaea
– found in marine bacterioplankton using DNA sequence
analysis of uncultivated organisms
– also found in cyanobacteria
36
3. Thermoplasms
• Class Thermoplasmata
• Three different genera
– Thermoplasmataceae
– Picrophilaceae
– Ferroplasmataceae
• Thermoacidophiles
• Lack cell walls
37
Genus Thermoplasma
• Thermoacidophiles; grow in refuse piles of coal
mines at 55–59°C, pH 1–2, FeS
• Cell structure
– shape depends on temperature
– may be flagellated and motile
– cell membrane strengthened by diglycerol tetraethers
(caldarchaeol), lipopolysaccharides, and glycoproteins
– nucleosome-like structures formed by association of DNA
with histone-like proteins
38
Genus Picrophilus
• Irregularly shaped cocci, 1 to 5 M diameter
– large cytoplasmic cavities that are not membrane bound
– no cell wall
– has S-layer outside plasma membrane
• Thermoacidophiles
– 47–65°C (optimum 60°C)
– pH <3.5 (optimum 0.7)
• Aerobic
39
4. Extremely Thermophilic S0-Reducers
• Class Thermococci; one order, Thermococcales
• One family containing three genera, Thermococcus,
Paleococcus, Pyrococcus
• Motile by flagella
• Optimum growth temperatures 88–100°C
• Strictly anaerobic
• Reduce sulfur to sulfide
40
5. Sulfate-Reducing Euryarchaeota
• class Archaeoglobi; order Archaeoglobales; one family
with one genus, Archaeoglobus
• irregular coccoid cells
– cell walls consist of glycoprotein subunits
• extremely thermophilic (optimum 83°C)
– isolated from marine hydrothermal vents
• metabolism
– lithotrophic (H2) or organotrophic (lactate/glucose)
– use sulfate, sulfite, or thiosulfite as electron acceptor
– possess some methanogen coenzymes
41
Aciduliprofundum
• Newly characterized thermophilic euryarchaeote
– acidophile, requires pH 3.3 to 5.8
– thermophile, 60–75oC for growth
– inhabit hydrothermal vents
– sulfur- and iron-reducing heterotroph
• First thermoacidophile in sulfide rich areas
• May be important in iron and sulfur cycling
42
Homework
1. Define ‘organotrophy’, ‘lithotrophy’, ‘autotrophy’, and ‘phototrophy’.
2. Why do methogens use the reductive acetyl-CoA pathway for carbon fixation (Figure
3)? Given that the DC/HB pathway uses far less ATP per pyruvate synthesized than
the HP/MB pathway, why do some archaea use the HP/HB pathway instead?
Explain why the fixation of CO2 by Thermoproteus spp. using the DC/HB cycle is not
photosynthesis (Figure 20.4).
3. Why do haloarchaea use the methylaspartate rather than the glyoxylate cycle for
the incorporation of acetate? Why might the production of glutamate as an
intermediate be beneficial for some haloarchaea (Figure 20.5)?
4. Discuss the role of external pH on the magnitude of the proton motive force
generated by Sulfolobus spp. (Figure 20.11).
5. Define halophiles. How do halophiles cope with osmotic stress? What are the
functions of archaerhodopsins and sensory rhodopsins of Halobacterium
salinarum?
6. How do thermoplasmas, a group of archaea lacking cell walls, cope with high
temperatures and acidic pH?
43