This chapter summarizes the properties of a diverse group of organisms known as the archaea. These organisms are very different from the eubacteria and from the eicaryotes. The chapter describes some of the major characteristics associates with each of the major groups of archaea.

After reading this chapter you should be able to:

• discuss the morphological and physiological diversity of the archaea
• discuss the difference between the cell walls of archaea and those of eubacteria
• describe the lipid composition of archaeal cell membranes
• discuss the general genetic, molecular, and metabolic characteristics of the archaea
• discuss the restricted habitats that are typical for the archaea
• discuss the classification scheme for the archaea that will be used in the 2^nd edition of Bergey's Manual
• discuss the unique cofactors used by methanogenic and sulfate-reducing archaeobacteria for methanogenesis
• describe the structural, chemical, and metabolic adaptations that allow the archaea to grow in extreme environments

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 pleiomorphic
3. They may exist as single cells, aggregates or filaments
4. They may multiply by binary fusion, budding, fragmentation, or other mechanisms
5. They may be aerobic, facultively 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 prefer restricted or extreme aquatic and terrestrial habitats
9. Recently, archaeobacteria have been found in cold environments and may constitute up to 34% of the procaryotic biomass in Antarctic surface waters
10. A few are symbionts in animal digestive systems

1. Archaeal Cell Walls

1. Archaeal cell wall structure differs from that of eubacteria
2. Gram-positive archaeobacteria, like gram-positive eubacteria, have a cell wall that has a single homogeneous layer
3. Gram-negative archaeobacteria lack the outer membrane and complex peptidoglycn network associated with gram-negative eubacteria
4. The surface layer of archaeobacteria consists of protein or glycoprotein subunits
5. Archaeal cell wall chemistry is different from that of eubacteria

1. Lacks muramic acid and D-amino acids
2. Resistant to lysozyme and b -lactam antibiotics
3. Some have pseudomurein, a peptidoglycan-like polymer that has L-amino acids in its cross-links and different monosaccharide subunits and linkage
4. Others have different polysaccharides
5. Gram-negative archaeobacteria have a layer of protein or glycoprotein outside their plasma membrane

1. Archaeal Lipids and Membranes

1. Archaeobacterial lipids differ from those of eubacteria and eucaryotes; branched

hydrocarbons are attached to glycerol by ether links rather than straight-chain fatty acids

attached to glycerol by ester links

2. Other, more complex tetraether structures are also found
3. Membranes contain polar lipids such as phospholipids, sulfolipids, and glycolipids
4. Membranes also contain nonpolar lipids (7-30%) that are usually derivatives of squalene
5. Membranes of extreme thermophiles are almost completely tetraether monolayers

1. Genetics and Molecular Biology

1. Archaea have few plasmids
2. The genome of Methanococcus jannaschii has been completely sequenced

1. 56% of its 1,738 genes are unlike those in eubacteria or eucarya
2. These organisms, therefore, are as distinctive genotypically as they are in other respects

1. Archaeal mRNA is like that of eubacteria (i.e., it may be polygenic, there are no intron-

containing precursors, and its promotors are similar to those of eubacteria)

2. Archaeal tRNA contain modified bases not found in eubacterial tRNAs
3. Archaeal ribosomes have a different, more variable shape than those of eubacteria or eucarya
4. Archaeal ribosomes are the same size as eubacterial ribosomes but show antibiotic sensitivity similar to that of eucaryotic ribosomes
5. Archaeal RNA polymerase enzymes are more similar to eucaryotic enzymes than to eubacterial enzymes

1. Metabolism

1. Metabolic processes vary greatly among different groups
2. Archaea do not use the Embden-Meyerhof pathway for glucose catabolism; however they frequently use a reversal of that pathway for gluconeogenesis
3. Some (halophiles and extreme thermophiles) have a complete TCA cycle while others (methanogens) do not
4. Archaeal biosynthetic pathways appear to be similar to those of other organisms
5. Autotrophy is widespread with a variety of mechanisms for incorporating CO₂

1. Archaeal Taxonomy - shows great diversity

1. The current edition of Bergey's Manual divides the archaeobacteria into 5 groups
2. The new edition of Bergey's Manual will divide the archaea into two kingdoms

1. Euryarchaeota - described in four sections

1. methanogens
2. extreme halophiles
3. sulfate users
4. extreme thermophiles with sulfer-dependent metabolism

1. Crenarchaeota - divided into 3 orders

1. Thermoproteales - hyperthermophiles
2. Sulfolobales - thermoacidophilic
3. Igneococcales - hyperthermophiles that grow at neutral pH

1. Kingdom Crenarchaeota

1. Many are acidophiles and are sulfer-dependent; they are exremely thermophilic
2. Sulfer may be used as an electron acceptor in anaerobic respiration; or as an electron source by lithotrophs
3. Almost all are strict anaerobes
4. They grow in geothermally heated water or soils (solfatara) that contain elemental sulfer (sulfer-rich hot springs, waters surrounding submarine volcanic activity)
5. Some (e.g., Pyrodictum spp.) can grow quite well above the boiling point of water (optimum @ 105° C)
6. Some are organotrophic; others are lithotrophic
7. There are three orders and at least twelve genera; two of the better studied genera are Sulfolobus and Thermoproteus
8. Sulfolobus

1. Gram-negative, aerobic, irregularly lobed, spherical bacteria
2. Thermoacidophiles
3. Cell walls lack peptidoglycan but contain lipoproteins and carbohydrates
4. 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; however, they often grow lithotrophically on sulfer granules in hot springs oxidizing the sulfer to sulfuric acid

1. Long, thin, bent or branched rods
2. Cell wall is composed of glycoprotein
3. Strict anaerobes; they have temperature optima from 70-97° C and pH optima from 2.5 to 6.5
4. They grow in hot springs and other hot aquatic habitats that contain elemental sulfer
5. They grow organotrophically

1. They oxidize glucose, amino acids, alcohols, and organic acids
2. They carry out anaerobic respiration with elemental sulfer as the electron acceptor

1. They also can growlitotrophically using H₂ and S⁰
2. CO or CO₂ can serve as the sole carbon source

1. Kingdom Euryarchaeota

1. The Methanogens

1. Strict anaerobes that obtain energy by converting CO_2,, H₂, formate, methanol, acetate, and other compounds to either methane or to methane and CO₂
2. There are at least three orders and 25 genera, which differ greatly in shape, 16s rRNA sequence, cell wall chemistry and structure, membrane lipids, and other features
3. Metabolism is unusual; members of this group contain several unique cofactors, some of which are associated with methane production
4. They thrive in anaerobic environments rich in organic matter, such as animal rumens 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. There may be an ecological problem though; 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

1. The Halobacteria - extreme halophiles

1. Consists of nine genera in one family, the Halobacteriaceae
2. They are aerobic chemoheterotrophs with respiratory metabolism; they require complex

nutrients

3. They require at least 1.5 M NaCl and have growth optima near 3-4 M NaCl
4. If the NaCl concentration drops below 1.5 M the cell walls disintegrate
5. They can cause spoilage of salted foods
6. Halobacterium salinarum has a unique type of photosynthesis that uses a modified cell membrane (called the purple membrane) which contains the protein, bacteriorhodopsin, but no chlorphyll
7. 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
8. Halorhodopsin uses light energy to transport chloride ions into the cell to maintain an 4-5 M intracellular Kcl concentration

1. The Thermoplasms

1. Thermoacidic cocci that lack call walls
2. Thermoplasma has an optimum temperature of 55-59° C and an optimal PH of 1 to 2
3. At 59° C Thermoplasma takes the form of an irregular filament; the cells may be flagellated and motile
4. Frequently found in coal mine refuse, in which chemolithotrophic bacteria oxidize iron pyrite to sulfuric acid and thereby produce a hot acidic environment
5. They have no cell wall but the cell membrane is strengthened by large quantities of diglycerol tetraethers, lipopolysaccharides, and glycoproteins
6. Their DNA is stabilized by its association with histonelike proteins, which form particles resembling eucaryotic nucleosomes
7. Picrophilus also has no cell wall but has an S-layer outside the plasma membrane
8. Picrophilus has large cytoplasmic cavities that are not membrane bounded
9. Picrophilus is aerobic and grows between 47° C and 65° C with an optimum of 60° C; it grows only below pH 3.5, has an optimum of pH 0.7 and will even grow at or near pH 0

1. The Thermococci

1. There are three orders, Archaeogobales, Thermococcales and Methanopyrales
2. All have cell walls
3. Thermococcales are strictly aerobic, reduce sulfur to sulfide, are motile by means of flagella, and have optimum growth temperatures around 88-100° C
4. Archaeogobales are gram-negative, irregular coccoid cells with walls of glycoprotein subunits; they cannot use elemental sulfur and are extremely thermophilic (optimum around 83° C); they are usually found near marine hydrothermal vents
5. Methanopyrales have an optimum temperature of 98° C and will grow at 110° C' they have been isolated from a marine hydrothermal vent; evidence suggests that they may be among the first living organisms to have developed