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General Microbiology II

Archaeal Diversity Study Guide

General Characteristics of Archaea

• Morphology
  • Prokaryotic - 0.1-15 x 0.1-200 µm (typically, 0.3-1 x 0.3-6 µm)
  • Membranes - structure similar to that found in Bacteria and Eukarya, but Archaea use ether linkages in lipids (rather than ester linkages) and form:
    • bilayer membranes from glycerol-diethers
    • monolayer membranes from diglycerol-tetraethers (thermal stability?)
  • Cell wall
    • protects the cytoplasm from osmotic pressure changes and provides cell shape - bacillus; coccus; lobed or irregular spheres (no cell wall)
    • Gram-positive or Gram-negative, lacks peptidoglycan (no muramic acid or D-amino acids); instead, possess:
      • pseudopeptidoglycan - alternating repeats of N-acetylglucosamine and N-acetyltalosaminuronic acid (1-3 links, lysozyme resistant) with 7-member L-amino acid cross-links (Methanobacterium)
      • polysaccharide - thick polymers containing galactosamine, glucuronic acid, glucose and acetate (Methanobacterium) or sulfated glucose, glucoseamine, mannose, mannoseamine, galactose and galactosamine (Halococcus)
      • glycoprotein - negatively charged proteins with many acidic residues (especially aspartic acid) "decorated" with polymers of glucose, glucoseamine, mannose, galactose, ribose and arabinose (extreme halophiles, Halobacterium; extreme thermopliles, Sulfolobus, Pyrodictium)
      • protein - single polypeptide subunit that forms a sheath (Methanospirillum) or several distinct polypeptide subunits (Methanococcus, Methanomicrobium)
  • Ribosomes - small RNA/protein particles which are required for protein synthesis (act more like those of Eukarya (sensitive to anisomysin, insensitive to chloramphenicol and kanamycin) than those of Bacteria, even though they are 70S); EF-2 is sensitive to diphtheria toxin
  • 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
  • Granules - intracytoplasmic storage bodies (glycogen)
  • Endospores - not formed
  • Capsules - polysaccharide "coatings" secreted by cells (???)
  • Flagella- very long protein (flagellin) polymers that provide motility
  • Pili - long thin protein (pilin) polymers that act as cell "anchors" to various surfaces and can assist in attaching archaeal cells to facilitate DNA transfer from one to the other
• Genetics
  • Gene exchange - mediated by plasmids via conjugation (transduction? or transformation?)
  • Operons - probably present, since Archaea have polycistronic mRNA; these coordinately controlled groups of genes use typical on/off signals (TATA box, Pribnow box, Shine-Dalgarno sequence, etc.)
  • Introns - like those found in Eukarya (none are found in Bacteria)
  • RNA polymerases behave more like those of Eukarya (large, complex, resistant to rifampin)
• Reproduction - asexual, via binary fission, budding, fragmentation
• Physiology
  • Physical requirements
    • temperature - most are thermophiles, some are extreme thermophiles
    • oxygen - aerobic or anaerobic
    • pH - many "prefer" acid conditions; extreme halophiles "prefer" alkaline conditions
    • salts - some extreme halophiles (require high salt concentration for growth)
  • Absorptive nutrition - some require growth factors
    • organotrophic - most are strict aerobes which derive energy from catabolism of organic molecules
    • lithotrophic - anaerobes which derive energy and carbon from methanogenesis
    • phototrophic - some Halobacterium species synthesize ATP using a bacteriorhodopsin system (not photosynthesis)
  • Metabolism - varies greatly among groups
    • TCA cycle and electron transport system (ETS) - fairly typical in halophiles and thermophiles, but not in methanogens
    • ATP synthesis via:
      • chemiosmotic mechanisms - proton gradient and membrane-bound ATP synthase utilized for phosphorylation; some use final electron acceptors other than oxygen (nitrate, oxidized sulfur etc.)
      • substrate-level phosphorylation - all organotrophs use it some
• Habitat - generally in extreme habitats (swamps, salt lakes, acidic hot springs)
  • Extreme thermophiles (Thermoplasma, Sulfolobus) are sulfur-dependent acidophiles with temperature optima of greater than 50C (extreme thermophiles prefer temperatures greater than 70C)
  • Extreme halophiles (Halobacterium, Halococcus) require high salt for growth
  • Methanogens are generally found in anaerobic environments rich in organic matter
• Importance
  • Reduced carbon source - lithotrophs and phototrophs generate basic nutrients for smallest animals
  • Symbionts - e.g., rumen of cattle, etc.
  • Saprophytic - organotrophs are generally decomposers

Groups of Archaea

Euryarchaeota (Phylum I)

• Extreme Halophiles
  • Gram-negative - many have yellow-to-red carotenoid pigments that protect them against sunlight
    • rods (0.6-1 x 1-6 µm) with glycoprotein walls (Halobacterium, motile via lophotrichous flagella; Natronobacterium)
    • cocci (0.6-1.5 µm) with sulfated polysaccharide walls (Halococcus, Natronococcus)
    • flattened disks or cup-shapes (Haloferax)
    • irregular disks, triangles, rectangles (Haloarcula)
  • Organotrophic aerobes that require very high salt (1.5-5.5 M, prefer 3-4 M) and require complex nutrients (vitamins, etc.) for growth (fastidious)
    • potassium ions bind to acidic proteins, rather than organic compatible solutes, to prevent dehydration
    • amino acids, organic acids or carbohydrates (modified Entner-Duodoroff pathway) are used for energy (via TCA cycle, respiratory metabolism)
    • anaerobic respiration used by some Halobacterium species with nitrate, sulfur, thiosulfate as terminal electron acceptors
    • ATP synthesized by other Halobacterium species using a light-mediated bacteriorhodopsin/retinal system
  • Hypersaline aquatic environments with alkaline pH such as Great Salt Lake, Dead Sea, solar salt evaporating ponds (salterns) and salted fish, are the normal habitat for these Archaea
• Methanogens
  • Gram-negative or Gram-positive - some have pseudopeptidoglycan, some have protein, some have polysaccharide cell walls; coenzyme F420 fluorescence used for identification of methanogens; 3 orders and 13 genera based on 16S rRNA structure
    • long (Methanobacterium, Methanothrix) or short (Methanobrevibacter) rods (0.5-1 µm wide) that occur as very long filaments
    • cocci (1.5-2.5 µm) that occur in singlets (Methanococcus), aggregates (Methanolobus), packets (Methanosarcina), or chains (Methanopyrus)
    • spirals (Methanospirillum)
    • plate-shaped (Methanoplanus)
  • Strictly anaerobic, fastidious (require vitamins, amino acids, nickel {part of coenzyme F430, hydrogenase, carbon monoxide dehydrogenase}, iron, cobalt); Methanopyrus is an extreme thermophile; no known methanogens have a complete TCA cycle; some can fix nitrogen
    • lithotrophs - generate methane using hydrogen and carbon dioxide that is fixed via a reductive acetyl-CoA pathway (Methanobacterium, Methanothermus, Methanococcus, Methanogenium, Methanoplanus)
    • organotrophs - generate methane from methyl groups of formate, methanol (Methanosphaera, Methanosarcina, Methanococcoides) or acetate (Methanothrix, Methanosaeta)
  • Environments rich in organic matter such as anaerobic sewage digestors, anoxic freshwater sediments and the rumen of cattle are normal habitats for these Euryarchaeota; they are very important as sources of methane (natural gas)
• Extreme Thermophiles
  • Gram-negative
    • rods (Methanopyrus)
    • filaments (Thermofilum)
    • spheres that are motile via lophotrichous flagella (Thermococcus, Pyrococcus)
  • Obligate anaerobes that require temperatures above 70C for growth and use sulfur as electron acceptor
    • organotrophs - use a modified Entner-Duodoroff pathway to oxidize organic compounds for energy (oxygen or sulfur serves as final electron acceptor)
      • organic compound + S H₂S + CO₂ (Thermococcus,Thermofilum, Pyrococcus)
      • organic compound CO₂ + H₂ (Pyrococcus)
    • lithotrophs
      • carbon dioxide fixation occurs via reductive (reverse) acetyl-CoA pathway
        • Methanopyrus - oxidizes hydrogen for energy (4 H₂ + carbon dioxide yields methane + 2 water) and fixes carbon dioxide at the same time (thermophilic methanogen)
      • some are lithoorganotrophs that can also grow organotrophically using sulfur as an electron acceptor (see above)
  • Geothermally heated acidic soils or waters which contain sulfur (solfatara), such as those in Yellowstone National Park and near marine hydrothermal vents are the usual habitats for these Euryarchaeota
• Sulfate Reducers (Archaeoglobus)
  • Gram-negative irregular motile spheres
  • Thermophilic (83C is optimum) anaerobes that can extract electrons from hydrogen, lactate, glucose, etc. and reduce sulfate, sulfite, or thiosulfate to sulfide via anaerobic respiration, but are also weakly methanogenic (share many genes with methanogens)
  • High-temperature, sulfate-containing environments such as marine hydrothermal vents are the usual habitats for these Euryarchaeota
• Wall-Less Archaea (Thermoplasma)
  • No cell wall (resemble mycoplasmas)
    • single triple-layered membrane that contains glycoproteins plus lipopolysaccharide consisting of tetraether lipid with mannose and glucose
    • irregular filamentous shape at or above 59C, spherical (0.3-2 µm) below 59C
    • very small genome, with DNA surrounded by histone-like DNA-binding proteins
    • budding is mode of reproduction
  • Acidophilic thermophilic aerobic organotroph
  • Coal refuse piles which are heated and made acidic by (other) lithotrophic bacteria which oxidize iron pyrite (FeS) to sulfuric acid are the only habitats in which these Euryarchaeota are found in nature

Crenarchaeota (Phylum II)

• Most Crenarchaeota are extreme thermophiles with growth optima at temperatures greater than 80C
  • Gram-negative
    • rods (Thermoproteus)
    • disc-shapes (Thermodiscus)
    • filaments (Thermofilum)
    • irregular (lobate) spheres 0.8-1 µm in diameter (Sulfolobus)
    • spheres that are motile via lophotrichous flagella (Staphylothermus)
  • Obligate anaerobes that require temperatures above 70C for growth and use sulfur as electron acceptor (except Sulfolobus, which uses oxygen or ferric iron)
    • organotrophs - use a modified Entner-Duodoroff pathway to oxidize organic compounds for energy (oxygen or sulfur serves as final electron acceptor)
      • organic compound + S H₂S + CO₂ (Thermoproteus, Desulfurococcus, Thermofilum, Pyrococcus)
      • organic compound + O₂ H₂O + CO₂ (Sulfolobus)
      • organic compound CO₂ + fatty acids (Staphylothermus)
    • lithotrophs - can also grow organotrophically using sulfur as an electron acceptor (see above)
      • Pyrodictium - optimum temperature, 105C; uses hydrogen as energy source, sulfur as electron acceptor (H₂ + S H₂S) and carbon dioxide as carbon source (via a reverse (reductive) acetyl-CoA pathway)
      • Sulfolobus - optimum temperature for growth, 70-80C; requires a pH of 2-3; aerobically oxidizes sulfur (2 S + 3 O₂ + 2 H₂O 2 H₂SO₄) and ferrous iron (4 FeS + 15 oxygen + 2 water 2 Fe₂(SO₄)₃ + 2 H₂SO₄) for energy; fixes carbon dioxide via a reverse (reductive) TCA cycle much like that seen in green sulfur bacteria
      • Thermoproteus - grows at 78-96C, pH 1.7-6.5; uses hydrogen as energy source, sulfur as electron acceptor (H₂ + S H₂S) and carbon dioxide as carbon source
  • most are anaerobic (respiratory) lithotrophs (Pyrodictium), organolithotrophs or organotrophs (Thermococcus, Thermoproteus) that require elemental sulfur for optimal growth (Desulfurococcus)
  • Sulfolobus is an aerobic organolithotroph
  • Geothermally heated, acidic soils or waters which contain sulfur (solfatara), such as those in Yellowstone National Park and near marine hydrothermal vents are the usual habitats for these Crenarchaeota
• Chere are also a number of as yet unidentified marine crenarchaeotes, including some cryophiles, that have been detected via community sampling of ribosomal RNA genes

Korarchaeota (Phylum III)

• recently discovered extreme thermophiles
• these are among the most primitive life forms discovered to date

Nanoarchaeota (Phylum IV)

• newly discovered ... only 1 genus: Nanoarchaeum
• very small (~0.4 um) coccoid parasitic (?) hyperthermotrophic (~90C) cells that replicate only when attached to Ignicoccus (a hydrogen-oxidizing crenarchaeote that reduces S) cells
• these are the most primitive life forms discovered to date