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  1. Introduction to the Archaea
    1. The archaea are quite diverse, both in morphology and physiology
      1. They may stain gram positive or gram negative
      2. They may be spherical, rod-shaped, spiral, lobed, plate-shaped, irregularly shaped or pleomorphic
      3. They may exist as single cells, aggregates or filaments
      4. They may multiply by binary fission, budding, fragmentation, or other mechanisms
      5. They may be aerobic, facultatively anaerobic, or strictly anaerobic
      6. Nutritionally, they range from chemilithoautotrophs to organotrophs
      7. Some are mesophiles, while others are hyperthermophiles that can grow above 100°C
      8. They are often found in extreme aquatic and terrestrial habitats; recently, archaea have been found in cold environments and may constitute up to 34% of the procaryotic biomass in Antarctic surface waters; a few are symbionts in animal digestive systems
    2. Archaeal cell walls
      1. Archaea can stain either gram positive or gram negative, but their cell wall structure differs significantly from that of bacteria
        1. Many archaea that stain gram positive have a cell wall made of a single homogeneous layer
        2. The archaea that stain gram negative lack the outer membrane and complex peptidoglycan network associated with gram-negative bacteria
      2. Archaeal cell wall chemistry is different from that of bacteria
        1. Lacks muramic acid and D-amino acids and therefore is resistant to lysozyme and b-lactam antibiotics
        2. Some have pseudomurein, a peptidoglycan-like polymer that has L-amino acids in its cross-links and different monosaccharide subunits and linkage
        3. Others have different polysaccharides
      3. The archaea that stain gram negative have a layer of protein or glycoprotein outside their plasma membrane
    3. Archaeal lipids and membranes
      1. Lipids have branched hydrocarbons attached to glycerol by ether links rather than straight-chain fatty acids attached to glycerol by ester links as seen in Bacteria and Eucarya
      2. Other, more complex tetraether structures are also found
      3. Membranes contain polar lipids such as phospholipids, sulfolipids, and glycolipids and also contain nonpolar lipids (7-30%), which are usually derivatives of squalene
      4. Membranes of extreme thermophiles are almost completely tetraether monolayers
    4. Genetics and molecular biology
      1. The archaeal chromosomes that have been studied consist of a single, closed DNA circle like those of bacteria, except that some are considerably smaller; Archaea have few plasmids; genomic analysis suggests are as distinctive genotypically as they are in other respects
      2. Archaeal mRNA is like that of bacteria (i.e., it may be polygenic, there is no evidence of intron-containing precursors, and its promoters are similar to those of bacteria)
      3. There are many other differences between archaea and other organisms, including:
        1. The observation of modified bases in archaeal tRNA molecules that are not found in bacterial tRNA molecules
        2. Ribosomes with different morphological and physiological properties than bacterial and eucaryotic ribosomes
        3. Archaeal RNA polymerase enzymes that are more similar to eucaryotic enzymes than to bacterial enzymes
    5. Metabolism
      1. Carbohydrate metabolism is best understood
        1. Archaea do not use the Embden-Meyerhof pathway for glucose catabolism; however they frequently use a reversal of that pathway for gluconeogenesis
        2. Some (halophiles and extreme thermophiles) have a complete TCA cycle while others (methanogens) do not
      2. Archaeal biosynthetic pathways appear to be similar to those of other organisms
      3. Autotrophy is widespread; reductive TCA cycle and reductive Acetyl-CoA cycle are used for carbon fixation
    6. Archaeal Taxonomy-the new edition of Bergey’s Manual will divide the archaea into two phyla: Euryarchaeota and Crenarchaeota
  2. Phylum Crenarchaeota
    1. Many are extremely thermophilic, acidophilic, and sulfur-dependent
      1. Sulfur may be used as an electron acceptor in anaerobic respiration, or as an electron source by lithotrophs
      2. Almost all are strict anaerobes
      3. They grow in geothermally heated water or soils (solfatara) that contain elemental sulfur (sulfur-rich hot springs, waters surrounding submarine volcanic activity); some (e.g., Pyrodictum spp.) can grow quite well above the boiling point of water (optimum @ 105oC)
      4. Some are organotrophic; others are lithotrophic
      5. There are 69 genera; two of the better-studied genera are Sulfolobus and Thermoproteus
    2. Sulfolobus
      1. Stain gram negative; are aerobic, irregularly lobed, spherical bacteria
      2. Thermoacidophiles
      3. Cell walls lack peptidoglycan but contain lipoproteins and carbohydrates
      4. Oxidize sulfur to sulfuric acid; oxygen is the normal electron acceptor, but ferric iron can also be used
      5. Sugars and amino acids may serve as carbon and energy sources
    3. Thermoproteus
      1. Long, thin, bent or branched rods
      2. Cell wall is composed of glycoprotein
      3. Strict anaerobes
      4. They have temperature optima from 70-97°C and pH optima from 2.5 to 6.5
      5. They grow in hot springs and other hot aquatic habitats that contain elemental sulfur
      6. They carry out anaerobic respiration using organic molecules as electron donors and elemental sulfur as the electron acceptor; they can also grow lithotrophically using H2 and S0 as electron donors and CO or CO2 as the sole carbon source
  3. Phylum Euryarchaeota
    1. The Methanogens
      1. Strict anaerobes that obtain energy by converting CO2, H2, formate, methanol, acetate, and other compounds to either methane or to methane and CO2; there are at least five orders, which differ greatly in shape, 16S rRNA sequence, cell wall chemistry and structure, membrane lipids, and other features
      2. Methanogens belonging to the order Methanopyrales have been suggested to be among the earliest organisms to evolve on Earth
      3. Methanogenesis is an unusual metabolic process and methanogens contain several unique cofactors
      4. They thrive in anaerobic environments rich in organic matter, such as animal rumens and intestinal tracts, freshwater and marine sediments, swamps, marshes, hot springs, anaerobic sludge digesters, and even within anaerobic protozoa
      5. They are of great potential importance because methane is a clean-burning fuel and an excellent energy source
      6. They may be an ecological problem, however, because methane is a greenhouse gas that could contribute to global warming and also because methanogens can oxidize iron, which contributes significantly to the corrosion of iron pipes
    2. The Halobacteria
      1. A group of extremely halophilic organisms divided into 15 genera
        1. They are aerobic chemoheterotrophs with respiratory metabolism; they require complex nutrients
        2. Motile or nonmotile by lophotrichous flagella
      2. They require at least 1.5 M NaCl and have growth optima near 3-4 M NaCl (if the NaCl concentration drops below 1.5 M the cell walls disintegrate; because of this they are found in high-salinity habitats and can cause spoilage of salted foods
      3. Halobacterium salinarum uses four different light-utilizing rhodopsin molecules
        1. Bacteriorhodopsin uses light energy to drive outward proton transport for ATP synthesis; thus they carry out a type of photosynthesis that does not involve chlorophyll
        2. Halorhodopsin uses light energy to transport chloride ions into the cell to maintain a 4-5 M intracellular KCl concentration
        3. Two other rhodopsins act as photoreceptors that control flagellar activity to position the bacterium in the water column at a location of high light intensity, but one in which the UV light is not sufficiently intense to be lethal
      1. The Thermoplasms
        1. Thermoacidic organisms that lack cell walls; only two genera are know: Thermoplasma and Picrophilus
        2. Thermoplasma
          1. Frequently found in coal mine refuse, in which chemolithotrophic bacteria oxidize iron pyrite to sulfuric acid and thereby produce a hot acidic environment
          2. Optimum temperature for growth of 55-59°C and an optimal PH of 1 to 2
          3. Cell membrane is strengthened by large quantities of diglycerol tetraethers, lipopolysaccharides, and glycoproteins
          4. Histonelike proteins stabilize their DNA; DNA-protein complex forms particles resembling eucaryotic nucleosomes
          5. At 59oC Thermoplasma takes the form of an irregular filament; the cells may be flagellated and motile
        3. Picrophilus
          1. Isolated from hot solfateric fields
          2. Has an S-layer outside the plasma membrane
          3. Irregularly shaped cocci with large cytoplasmic cavities that are not membrane bounded
          4. Aerobic and grows between 47°C and 65°C with an optimum of 60°C
          5. It grows only below pH 3.5, has an optimum of pH 0.7 and will even grow at or near pH 0
      2. Extremely thermophilic S0 metabolizers
        1. Strictly anaerobic, reduce sulfur to sulfide
        2. Are motile by means of flagella
        3. Have optimum growth temperatures around 88-100°C
      3. Sulfate-reducing archaea
        1. Gram-negative, irregular coccoid cells with walls of glycoprotein subunits
        2. Use a variety of electron donors (hydrogen, lactate, glucose) and reduce sulfite, sulfate, or thiosulfate to sulfide
        3. Are extremely thermophilic (optimum around 83°C); they are usually found near marine hydrothermal vents
        4. Contain two methanogen coenzymes





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