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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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IntroductionArchaea 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

- (1,3) linkages instead of (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 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

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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

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Archaeal Genomes

Unique features of Archaea- “Reverse gyrase” of hyperthermophiles

- Maintains positive supercoilsSimilarities 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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Transcription factor B (TFB)

RNA polymerases in Archaea behave more like those of Eukarya

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Phylogeny of ArchaeaThe 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

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Figure 19.5

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CrenarchaeotaThe 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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CrenarchaeotaDesulfurococcales

- 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

Organic-C + S0 H2S + CO2 + H2O

H2 + S0 H2S

D. mobilis

I. islandicus

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CrenarchaeotaBarophilic

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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CrenarchaeotaSulfolobales (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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CrenarchaeotaAlso 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: MethanogensEuryarchaeota 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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Methanogens grow in:- Anaerobic soil of wetlands

- Especially rice paddies

- Landfills

- Digestive tracts of animals

- Termites

- Cattle

- Humans

- Marine benthic sediments

Anaerobic Habitats for Methanogens

Figure 19.22A

Figure 19.22B

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Biochemical pathways of methanogens involve unique cofactors.

- These transfer the hydrogens and increasingly reduced carbon to each enzyme in the pathway.

Biochemistry of Methanogenesis

Figure 19.25

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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.

Biochemistry of Methanogenesis

Figure 19.26

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Euryarchaeota: HalophilesMain inhabitants of high-salt environments are

members of the class Haloarchaea.

- 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

Figure 19.28

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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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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

Habitats for Haloarchaea

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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: ThermophilesThermococcales

- 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 19.33A

Figure 19.33B

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Figure 19.34

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Euryarchaeota: AcidophilesThermoplasmatales

- 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

- Is an obligate symbiont of the crenarchaeote Ignicoccus hospitalis

- Host and symbiont genomes have been sequenced, revealing extensive coevolution.

Figure 19.36

Nanoarchaeum equitans

The smallest known euryarchaeotes.

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Deeply Branching DivisionsNew 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