Chapter 19: Archaeal Diversity
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Transcript of Chapter 19: Archaeal Diversity
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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 TraitsThe 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 LipidsAre 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 PathwaysGlucose 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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CrenarchaeotaSulfolobus
- 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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CrenarchaeotaThe 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-layersb) Supercoiled DNAc) Thermophilesd) Pseudopeptidoglycan