Archaea

Prokaryotes are divided into two domains, bacteria and archaea, based on the lack of a membrane bound nucleus. Archaea and bacteria are morphologically similar and can’t be distinguished by microscopy but there are fundamental differences between the two groups which mean that archaea are actually more closely related to Eukaryota. None of these groups are ancestral to the others, they all diverged before becoming what they are today so the term ‘archaea’ is perhaps misleading as it suggests archaea to be archaic, perhaps more simple structures. The term ‘prokaryote’ is becoming a more controversial term as it doesn’t reflect evolutionary history and it only tells us what an organism doesn’t have, rather than what it has.

Gram positive bacteria are monoderm, meaning they have a single membrane whereas Gram negative bacteria are diderm meaning they have two membranes. Archaea are monoderms like Gram positive bacteria. However the archaeal membrane is more chemically and structurally diverse. It is a semi-rigid lattice of pseudomurein, sugars, proteins or glycoproteins. The S layer, a protein layer contributing to rigidity, is a very common arrangement for archaea.

Bacteria and eukaryotes have the same isomer of glycerol, 1,2-sn-glycerol aka D-glycerol, in their membranes whereas archaeal membranes contain 2,3-sn-glycerol aka L-glycerol. Bacterial phospholipids contain ester linkages whereas archaeal phospholipids contain ether linkages. Some archaea have a monolayer rather than a bilayer. Lipid sidechains are branched isoprene chains in archaea whereas they are unbranched fatty acids in bacteria and eukaryotes.

Bacterial flagella are helical filaments which rotate, allowing motility. Archaeal flagella are similar in appearance to bacterial flagella but have a completely different protein sequence among other differences, and are considered non-homologous. This is an example of convergent evolution which is the independent evolution of similar structures in different species - essentially ‘different method, same result’. Archaeal flagella grow by addition to their bases whereas bacterial flagella are produced in a more complex way by addition of flagellin subunits at the tip. Bacterial flagella are hollow to allow flagellin subunits to pass through, and they are also thicker than archaeal flagella.

Both bacteria and archaea have plasmids, are unicellular and arrange their genes in operons. Both archaea and eukaryotes are insensitive to antibiotics, are sensitive to diphtheria toxin, arrange their DNA by histones and have complex DNA and RNA polymerases.

Archaea are split into five major groups: Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota and Nanoarchaeota. Some of these groups (Nano and Korarchaeota) only contain one genus, this is due to archaea being understudied and difficult to culture rather than the group actually only containing just 1.

Euryarchaeota are a physiologically diverse group. Many inhabit extreme environments with high temperatures, high salt or high acid content. Key genera are Halobacterium, Haloferax and Natronobacterium. Named ‘bacteria’ as they were discovered before it was realised archaea were a separate group. These archaea are extremely halophilic and typically require a minimum of 1.5M (approx 9%) NaCl for growth. Found in artificial saline habitats, solar salt evaporation ponds and salt lakes. They reproduce by binary fission and don’t form resting stages or spores. Most are nonmotile and obligate aerobes. They are adapted for life in highly ionic environments eg have a very thick cell wall composed of glycoprotein which is stabilised by sodium ions. Many are coloured due to production of bacteriorhodopsin.

Halophiles usually maintain osmotic balance by accumulation or synthesis of compatible solutes such as glycerol. However, Halobacterium species instead pump large amounts of potassium ions into the cell from the environment. Therefore intracellular [K+] exceeds extracellular [Na+] to maintain positive water balance. Halophile proteins are highly acidic and contain fewer hydrophobic amino acids and lysine residues. Some haloarchaea are capable of light-driven ATP synthesis due to bacteriorhodopsin.

Key genera of methanogenic archaea are Methanobacterium, Methanocaldococcus and Methanosarcine. These produce CH4 and are found in many diverse environments. Their taxonomy is based on phenotypic and phylogenetic features. Methanogenic archaea have very diverse cell wall chemistries eg Methanobacterium cell wall = pseudomurein, Methanosarcina cell wall = methanochondroitin, Methanocaldococcus cell wall = protein/glycoprotein and Methanospirillum = S layer. Methanogens are obligate anaerobes and have 11 substrates of 3 different classes which can be converted to methane by pure methanogen cultures. Other compounds such as glucose can be converted to methane but only in cooperative reactions between methanogens and anaerobic bacteria.

Key genera of thermoplasmatales, a taxonomic order within Euryarchaeota, are Thermoplasma, Picrophilus and Ferroplasma. They are thermophilic and/or extremely acidophilic. Thermoplasma and Ferroplasma lack cell walls. Thermoplasma are chemoorganotrophs and are facultative aerobes via sulphur respiration. They are thermophilic, acidophilic and found in self-heating coal piles.

Thermoplasma have evolved unique cytoplasmic membrane structure to maintain positive osmotic pressure and tolerate high temperatures and low pH levels. Their membrane contains lipopolysaccharide-like material (lipoglycan) consisting of tetraether lipid monolayer membrane with mannose and glucose. The membrane contains glycoproteins but not sterols.

Ferroplasma are chemolithotrophic and acidophilic. They oxidise Fe (II) to Fe (III) ions, generating acid. They grow in mine tailings containing pyrite (FeS2) - this is why acid mine drainage occurs.

Picophilus are extreme acidophiles which grow optimally at pH 0.7. They are a model microbe for extreme acid tolerance.

Key genera of Thermococcales and Methanopyrus are Thermococcus, Pyrococcus and Methanopyrus. They are three phylogenetically related genera of hyperthermophilic Euryarchaeota. These genera comprise a branch near the root of the archaeal tree meaning they’re closely descended from more ancient life forms. The distinct order which contains Thermococcus and Pyrococcus is highly motile and indigenous to anoxic thermal waters. Uses in biotechnology include PCR.

Most crenarchaeota are obligate anaerobes. They are chemoorganotrophs or chemolithotrophs with diverse electron donors and acceptors. Most cultured representatives are hyperthermophiles found in extreme heat environments or extreme cold environments.

Key genera of crenarchaeota from terrestrial volcanic habitats are Sulfolobus, Acidianus, Thermoproteus and Pyrobaculum. Sulfolobales grow in sulphur-rich acidic hot springs and are aerobic chemolithotrophs which oxidise reduced sulphur or iron. Acidianus also live in acidic sulphur hot springs and use elemental sulphur both aerobically and anaerobically.

New thermophile and hyperthermophile species are being discovered and lab experiments with biomolecules suggest the upper temperature limits for life to be approx 140 to 150 degrees celsius. High concentrations of cytoplasmic solutes have a protective effect on protein monomer stability. More thermophilic species use more heat stable molecules eg non-heme iron proteins instead of proteins which use NAD and NADH. Amino acid composition is similar to non-thermostable proteins but structural features such as highly hydrophobic cores and increased ionic interactions on protein surfaces improve thermostability. High intracellular solute levels stabilise DNA as does reverse DNA gyrase, which is solely found in hyperthermophiles and introduces positive supercoils. High levels of intracellular polyamine eg putrescince and spermidine stabilise RNA and DNA and DNA-binding proteins (histones) compact DNA into nucleosome-like structures. Thermophiles have dibiphytanul tetraether type lipids which form a lipid monolayer membrane structure. Higher GC content = small subunit rRNA stability.

Hyperthermophiles may be the closest descendants of ancient microbes. Hyperthermophilic archaea and bacteria are found on the deepest, shortest branches of the phylogenetic tree. H2 oxidation is common to many hyperthermophiles and this may have been the first energy yielding metabolism.