The earliest discovered archaea were all living in high-temperature, high-salinity, and strong acid environments, and these environments have little relation to normal organisms and humans. Therefore, they were regarded for a long time as organisms that had lost the competition with bacteria. Only when archaea were detected in the Hydrothermal Vent in the deep sea floor did people realize how similar their habitats were to the primitive Earth. Archaea maybe play an important role in biological evolution. In fact, archaea are also distributed in moderate environments, such as soil, animal intestines, and mouths.
Methanogens without glycolysis are extremely anaerobic
The first identified archaea were methanogens. They may be the earliest lives that born at a certain hydrothermal vent. Because various reductive substances are very abundant in primitive ocean while sugars are almost absent, their metabolism is very different from modern organisms: methanogens cannot get energy from glucose; methanogens are extreme anaerobes, not only a trace of oxygen will kill them, but also the redox potential of external environment must be lower than -350mv (a large amount of reductive substances, such as hydrogen gas, ferrous ions, methane, etc.). Thus, anaerobic environments rich in organic matter are their favorite paradise: the digestive systems of ruminants, sediments in lakes, rivers, oceans, swamps and wetlands.
Organic matter is decomposed by other microbes into hydrogen, carbon dioxide, and some short-chain fatty acids and alcohols, and oxygen is exhausted. Then, methanogens use these to create a proton gradient to synthesize ATP. The expelled methane is equivalent to waste gas, just like carbon dioxide in aerobic respiration. The intermediate substance acetyl-CoA is used to synthesize amino acids, carbohydrates, and lipids. Sometimes, methane accumulates into bubbles that rise to the lake or pond surface. A significant part of atmospheric methane is contributed by these archaea.
Organic waste are often degraded by methanogen to reduce at least half of its mass. These residues contain hard-to-degrade organic matter (such as cellulose and lignin) that is often used as fertilizer or soil conditioner.
Photophosphorylation, Halophilic Archaea and Salt Lakes
Next discovered were halophilic archaea or haloarchaea. They live in water environments with salinity of 10-30%, such as the Dead Sea in Israel or Utah's Great Salt Lake in the United States. If the salinity is below 10%, they may not survive. Hydrophilic amino acids, glycerol, monosaccharides, and other substances accumulate within them to make cytoplasm isotonic to the external environment. These small molecules maintain cellular water but do not change protein conformation. Haloarchaea also possess specially structured proteins that are only active in high salinity. Since some salt comes from carbonate, the lake water is alkaline. Some lakes with high evaporation rates usually have a pH around 10.
Besides getting energy from organic matter, some halophilic archaea can also harvest energy from sunlight. Rhodopsin is excited by green light into a cis-structure and pumps protons into the space between plasma membrane and cell wall to create a proton concentration gradient. Rhodopsin then returns to its original trans-structure and prepares for the next excitation. When protons flow through ATPase, solar energy is stored in ATP. This is the simplest photophosphorylation involving only ATP and ADP, which is similar to the light-dependent reaction in photosynthesis but lacks the respiratory chain to transport electrons. However, haloarchaea only perform photophosphorylation or carbon fixation outside the C3 pathway, and the two metabolism have not been coupled to be a true photosynthesis. Since green light is absorbed, these red or purplish archaea dye salt lakes the same color.
PCR and Thermophile Indestructible by Boiling Water
If temperature exceeds 40-50°C, the proteins and cell membranes of many organisms will undergo thermal denaturation and lose function. However, the minimum survival temperature for thermophilic archaea or thermophile reaches around 40-50°C. Usually, the optimal temperature is between 50°C-80°C. Certain thermophile living in volcanic hot springs or hydrothermal vents in seafloor can withstand even higher temperatures. Their optimal temperature often close to boiling point of water. They cannot survive the temperature below 80°C. Strain 121 spent a day in the autoclave at 121°C, and its number even doubled. It was previously believed that all microorganisms exposed to this temperature would be killed, because it was temperature for medical equipment sterilization.
The greatest contribution of thermophilic archaea to humans is providing some thermostable DNA polymerase for PCR. The solution is heated above 90°C to separate DNA double helix due to the destroyed hydrogen bond, but Taq polymerase is temporarily inactive at this moment. When temperature drops to 72°C, the 2 single DNA strands acted as a template and free nucleotides are assembled into 2 new double-stranded DNA helixes with the help of Taq polymerase. This process is repeated 20-40 times to amplify DNA fragments exponentially.
Apart from extreme high temperatures, these thermophiles also endure low pH and oxygen. Sulfur dioxide released by crustal activity introduces sulfuric acid into water. Sometimes the pH value is even below 1, and it is equivalent to highly corrosive gastric acid of carrion-eating animals. Oxygen barely dissolves in nearly boiling water, so they respire anaerobically through sulfides and iron oxides that are common in undersea craters or hot springs.