1. 20
The Archaea
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2. 20.1 Overview of the Archaea
List some common habitats in which archaea reside
Describe the debate that surrounds archaeal taxonomy
Compare at least three key metabolic pathways that are central to archaeal physiology with those used by bacteria

3. Archaea Many features in common with Eukarya
genes encoding protein: replication, transcription, translation
Features in common with Bacteria
genes for metabolism
Other elements are unique to Archaea
unique rRNA gene structure
capable of methanogenesis

4. Archaea
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

5. Archaeal Taxonomy
Five major physiological and morphological groups

6. Archaeal Taxonomy Two phyla based on Bergey’s Manual
Euryarchaeota
Crenarchaeota
16S rRNA and SSU rRNA analysis also shows
Group I are Thaumarchaeota
Group II are Korachaeota

8. 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

9. Archaeal Metabolism Carbon fixation pathways include
Reductive acetyl-CoA pathway
3-hydroxyproprionate/4-hydroxybutyrate (HP/HB) cycle
Dicarboxylate/4-hydroxybutyrate (DC/HB) cycle

10. Archaeal Metabolism 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

11. Archaeal Metabolism
3-hydroxyproprionate/ 4-hydroxybutyrate (HP/HB) cycle
Requires more energy input (9 ATP/ pyruvate synthesized)
Can be operated under aerobic conditions
Has less of a demand for metal cofactors

12. Archaeal Metabolism Dicarboxylate/4- hydroxybutyrate (DC/HB) cycle
Consumes 5 ATP/pyruvate formed
Some of its enzymes are sensitive to oxygen
Steps are similar to a reversal of the TCA cycle

13. Carbohydrate Metabolism
Similarities in eukaryotes and bacteria
3 pathways unique to Archaea
modified Embden- Meyerhof
2 modified Entner- Duodoroff

14. Carbohydrate Metabolism
Similarities in eukaryotes and bacteria
3 pathways unique to Archaea
modified Embden- Meyerhof
2 modified Entner- Duodoroff

15. 20.2 Phylum Crenarchaeota
List the major physiological types among crenarchaea
Evaluate the importance of crenarchaeol in the discovery of new crenarchaeotes
Discuss hyperthermophilic and thermoacidophilic growth

16. 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

19. Crenarchaeota…
Include organotrophs and lithotrophs (sulfur- oxidizing and hydrogen-oxidizing)
Contains 25 genera
two best studied are Sulfolobus and Thermoproteus

20. Genus Thermoproteus Long thin rod, bent or branched Thermoacidophiles
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

21. Genus Sulfolobus Irregularly lobed, spherical shaped Thermoacidophiles
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

23. 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)

24. 20.3 Phylum Euryarchaeota
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
Discuss the physiology and ecology of anaerobic methane oxidation
Explain the strategies halophiles have evolved to cope with osmotic stress and why these strategies are needed
Outline rhodopsin-based phototrophy as used by halophiles
Describe the habitats in which methanogens and halophiles reside
List one unique feature for Thermoplasma, Pyrococcus, and Archaeoglobus

25. Phylum Euryarchaeota Consists of many classes, orders, and families
Often divided informally into five major groups
methanogens
halobacteria
thermoplasms
extremely thermophilic S0-metabolizers
sulfate-reducers

26. Methanogens All methanogenic microbes are Archaea Methanogenesis
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

27. Methanogens 26 genera, largest group of cultured archaea
differ in morphology
16S rRNA
cell walls
membrane lipids

29. Methanogens Unique anaerobic production of methane
hydrogen, CO2 oxidation
coenzymes, cofactors
ATP production linked with methanogenesis

31. 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

32. 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

33. Strategies to Cope with Osmotic Stress
Increase cytoplasmic osmolarity
use compatible solutes (small organics)
“Salt-in” approach
use antiporters/symporters to increase concentration of KCl and NaCl to level of external environment
Acidic amino acids in proteins

34. 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

36. Features of Halobacterium Rhodopsins
Bacteriorhodopsin
chromophore similar to retinal
seven membrane spanning domains
purple aggregates in membrane
Halorhodopsin
light energy to transport chloride ions
2 sensory rhodopsins
flagellar attached photoreceptors

38. 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

39. Thermoplasms Class Thermoplasmata Three different genera
Thermoplasmataceae
Picrophilaceae
Ferroplasmataceae
Thermoacidophiles
Lack cell walls

40. 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, lipopolysaccharides, and glycoproteins
nucleosome-like structures formed by association of DNA with histonelike proteins

41. 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

42. 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

43. 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

44. 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