1. Chapter 19: Archaeal Diversity

2. Chapter Overview ● Archaeal traits
● Crenarchaeota: Hyperthermophiles, Mesophiles, and psychrophiles
● Euryarchaeota: Methanogens, Halophiles, Thermophiles, and acidophiles
● Deeply branching divisions

3. 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.

4. Secret lives of archaea, tools to search for extraterrestrial life

5. 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

6. 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. 7

8. 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

9. Chromosome - single (closed circular) molecule of double-stranded 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

10. Archaeal Metabolic Pathways
Glucose is catabolized by several variants of the Entner-Doudoroff (ED) and Embden-Meyerhoff-Parnas (EMP) pathways that rarely occur in bacteria.
The process of methanogenesis is unique to Archaea.
Figure 19.3 10

11. 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

12. 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

13. RNA polymerases in Archaea behave more like those of Eukarya
Transcription factor B (TFB) 13

14. 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, alkalinophiles 14

15. Figure 19.5 15

16. 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

17. Table 19-3 Hyperthermophilic Crenarchaeota.

18. Crenarchaeota Desulfurococcales
- Lack cell walls, but have elaborate S-layer
- Reduce sulfur at higher temperatures
Desulforococcus mobilis
- Hot springs
Ignicoccus islandicus
- Marine organism 18

19. Hyperthermophiles: Desulfurococcales: Reduce sulfur from hot springs
Organic-C + S0  H2S + CO2 + H2O
H2 + S0  H2S
D. mobilis
I. islandicus

20. Crenarchaeota Grow at 100 –1200 C Reduce sulfur to H2S
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

21. Pyrodictium abyssi: cells linked by cannulae an example of single sp biofilm

22. Crenarchaeota H2S + 3O2 + 2H2O  2H2SO4
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

23. Crenarchaeota Sulfolobus sp. Sulfolobus
- No cell walls – only an S-layer of glycoprotein
- Membrane composed mainly of tetraethers with cyclopentane rings
Sulfolobus sp. 23

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. Haloarchaea are generally mesophilic.
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

35. 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

36. 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

37. Figure 19.31 37

38. Euryarchaeota: Thermophiles
Figure 19.33A
Thermococcales
- 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

39. Figure 19.34 39

40. 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

41. 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

42. 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

43. Chapter Summary - Euryarchaeota: Show a greater metabolism range
● 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

44. Chapter Summary - They inhabit anaerobic environments.
● 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

45. Pop Quiz Which of the following is unique to Archaea? a) S-layers
b) Supercoiled DNA
c) Thermophiles
d) Pseudopeptidoglycan
Answer: B 45