The extremists of life: the Archaea
The Archaea domain was not recognized as an important domain of the tree of life until recently. Until the 20th century, in fact, most biologists considered all living things classifiable as either plants or animals. But between the 1950s and 1960s, the taxonomists came to the realization that this method of classification is not accurate because such grouping cannot accommodate fungi, protists and bacteria.
From the 1970s, therefore, a set of five kingdoms ended up being accepted as the model by which all living things can be classified. In a nutshell, a distinction was made between prokaryotic bacteria and the four kingdoms of eukaryotes (plants, animals, fungi and protists). The distinction is based on the common traits that eukaryotic organisms share, such as nuclei, the Cytoskeleton and internal membranes.
The scientific community was then understandably shocked in the late 1970s by the discovery of a new group of organisms: the Archaea.
Dr. Carl Woese and his colleagues at the University of Illinois studied the relationships among prokaryotes using DNA sequences, and found that two distinctly different groups could be distinguished. Those "bacteria" that lived in fact at high temperatures they were far removed from the phylogenetic characteristics of bacteria (prokaryotes) and eukaryotic organisms. Because of this great genetic difference, Woese proposed that living organisms were divided into three groups: Eukaryota, Eubacteria, and Archaeobacteria. It was later decided that Archaeobacteria was a misnomer, and renamed as Archaea. Although most Archaea do not look so different from bacteria under the microscope, the extreme conditions in which many of these species live has made it difficult to culture and study. That is why for a long time nothing was known about their existence.
However, biochemically and genetically, they are very different from bacteria. Although many books and articles still refer to them as "archaeobacteria," that term has been dropped because they are not bacteria, they are Archaea.
Archaea live in some of the most extreme environments on the planet. They can survive in environments with temperatures above 100 °C, in the deep sea at high pressures, where they produce methane. Others live in hot springs, or in the Arctic and Antarctic oceans, which remain frozen for most of the year, or in extremely alkaline or acidic waters. They have been found inside the digestive tracts of cows and termites. They live in the anoxic sludge of swamps and thrive in deep oil deposits. They have even been found in automobile batteries!
Some Archaea can survive the dehydrating effects of extremely saline waters. One Archaea that has been studied extensively and lives well in saline environments is the group that includes the genus Halobacterium. This primordial life form is able to derive molecular energy in the form of ATP (adenosine triphosphate) from sunlight through a process of nonchlorophyll photophosphorylation made possible by bacteriorhodopsin, a protein abundant in the cytoplasmic membrane. Rhodopsin is a membrane protein with 7 transmembrane α-helical domains; it is mainly found in the rod cells of the human retina that enable black-and-white vision. These cells have an elongated shape and in their apical part have numerous membrane discs with many rhodopsins, bound via a Schiff base to a pigment, light-sensitive 11-cis-retinal.
Archaea may be the only organisms that can live in extreme habitats such as thermal chimneys or hypersaline waters. They can be extremely abundant in environments that are hostile to all other life forms. However Archaea are not just limited to extreme environments; recent research shows that Archaea are also very abundant in the plankton of the open sea. There is still much to learn about these microbes, but it is clear that Archaea is a remarkably diverse and successful group.
ARCHAEA FOSSILS
It is unusual to think that life could exist at temperatures near the boiling point, but some intrepid Archaea thrive in these extreme conditions. Geysers, such as those found in Yellow Stone Park, are habitats for many thermophilic microbes and may help us understand how life existed when Earth was still young.
The search for Archaea fossils faces a number of problems. First of all, they are very small organisms and therefore leave equally microscopic fossils. Any search for fossils of cells archaeals would require a lot of time under the microscope and just as much patience. In fact, there are known fossil microbes throughout the Precambrian, but there is a problem: how do you distinguish fossil Archaea from fossil bacteria? Archaea and bacterial cells can be the same size and shape, so the microbial outline of a fossil usually does not help determine its origin. Then there is a tendency to neglect the physical and micropaleontological characteristics of the organism, and to emphasize the chemical characteristics. Chemical traces of ancient organisms are called molecular fossils, and they include a wide range of chemicals. Ideally, a molecular fossil should be a chemical compound with the following characteristics: it is found in only one group of organisms, it is not subject to chemical degradation, it decays into predictable and recognizable secondary chemicals.
In the case of Archaea, there is a very good method for identifying a fossil of it, taking into account the molecular characteristics of its membrane cellular. The cell membranes of Archaea are not formed by lipids like other microorganisms, but are formed by isoprene chains. Because these isoprene structures make Archaea particular and unique, and they are not as prone to decomposition at high temperatures, they become good indicators for determining the presence of ancient Archaea. Molecular fossils of Archaea in the form of isoprenoid residues have been reported at the Messel site in Germany (Michaelis & Albrecht, 1979). These are deposits from the Miocene epoch, the geologic history of which is well known. Material taken from the site was dissolved and analyzed using a combination of chromatography and mass spectrometry. These processes for the separation of the compounds, favored the creation of a "chemical fingerprint." The Messel site fingerprint demonstrates an isoprene composition identical to that found in some Archaea. Based on the geologic history of the Messel area, it is believed that such thermophilic and halophilic organisms never lived there, so it is more likely that Archaea methanogens (methane-producing) left these chemical fingerprints.
Since their discovery in the Messel Shale, isoprene compounds indicative of ancient Archaea have been found in numerous other locations (Hahn & Haug, 1986), including Mesozoic, Paleozoic, and Precambrian sediments. Their chemical traces have even been found in the sediments of the Isua district of West Greenland, the oldest known sediments on Earth (about 3.8 billion years old). This means that Archaea (and life in general) appeared on Earth within a billion years of the planet's formation, and at a time when conditions were still quite inhospitable for life, as had hitherto been believed.
The atmosphere of the young Earth was rich in ammonia and methane, and it was probably very hot. Such conditions, toxic to present-day plants and animals, may instead have been very welcoming to Archaea. Rather than therefore being quirky organisms that evolved to survive in unusual conditions, Archaea may represent the remnants of a thriving biological community that significantly dominated and shaped our early world.
BIOLOGY OF ARCHAEA
Archaea can occur in spherical, stem, spiral, lobed, rectangular or irregularly shaped forms. An unusual, square-shaped, flat species lives in salt pools. Some exist as single cells, others form filaments or clusters. Their cell wall differs in structure from that of bacteria, so it has been thought that it may be more stable under conditions extreme, helping to explain why some Archaea can live in many of the most hostile environments on Earth.
These microorganisms, which form a kingdom of their own, survive in the ocean depths, with no light and little carbon, exploiting even very low concentrations of ammonia. Because of their ability to utilize ammonia, Archaea play a crucial role in the global nitrogen cycle and consequently also in the ecology of the planet. This is the finding published in the journal "Nature" by a team of researchers from the University of Washington led by David Stahl.
Ammonia is a product that can be toxic to animals. But several plants, including phytoplankton living in the shallowest layers of the sea, are able to use it as the most efficient way to produce new cells.
In the early 1990s, research on ocean water samples taken at depth revealed the presence of fragments of genetic material that suggested that at least 20 percent of the ocean's microorganisms are Archaea, while other evidence suggested that they could live off ammonia.
In 2005, Stahl's group was the first to isolate such an organism recovered from a tropical tank at the Seattle Aquarium, demonstrating how it can, in fact, grow by oxidizing ammonia. Since then, the organism has been found in many marine environments, including Puget Sound and the North Sea, and it is speculated that it may be nearly ubiquitous in marine waters.
This new work shows how Archaea can survive in the presence of extremely low ammonia concentrations, on the order of 10 nanomoles per liter of water, equivalent to one teaspoon of ammonia salts in 40 million liters of water, solving the long-standing mystery of how these microorganisms can survive in the ocean environment. For in the deep ocean there is no light and little carbon, and therefore these trace amounts of ammonia are the organism's only source of energy.
Archaea more specifically are anaerobic protobacteria: they extract sulfur from sulfates, which they bind to two hydrogen atoms of the three present in ammonia (NH3), releasing the nitrogen they need less, constituting a necessary phase of the nitrogen cycle, but releasing as waste sulfur with the two hydrogens, that is, H2S, or hydrogen sulfide. It is they who, living in the anoxic zones of the oceans, fill these zones with hydrogen sulfide, gigantic bubbles that, as long as they are held by the pressure of miles of water, do not frighten anyone, unless they are released by tectonic upheavals that, it is speculated, may have caused true mass extinctions.
BRIEF EVOLUTIONARY FRAMEWORK
The above has been quietly happening for millions of years; in fact, it is very likely that the Archaea are precisely the first life forms that evolved on the planet, almost more than 4.1 billion years ago. Shortly after the formation of the planet, such primitive organisms evolved by optimizing the exploitation of available energy, namely that of sulfates coming out of the bowels of the planet through powerful eruptions; for millions of years, then, the evolution of the Archaea goes on in this way, until the ancestors of the rhodophyceaea manage to carve out a small niche for themselves by beginning to exploit in the benthic zones the sunlight filtering from the atmosphere through photosynthesis, producing free molecular oxygen as waste.
As a consequence of random evolution, some bacteria will eventually specialize in capturing and utilizing free oxygen, while certain prokaryotes will incorporate such bacteria into their cytoplasm without until will evolve into the present-day mitochondria. At the same time, some forms of viruses specialize in processing increasingly complex nucleic acids: first into the most basic RNA elements and finally into DNA. We are now 3.9 billion years old. Eukaryotes using oxygen in cellular respiration with the Krebs cycle have now been formed and over the millions of years will eventually repel Archaea into relatively narrower niches. For more than 1 billion and assimilating them, half a year the planet has remained available to phyla that use free oxygen. One of these species has now colonized the planet, modifying it and altering its population balances, creating with its industrial processes new molecules that had never before been seen on the planet, such as aluminum itself, previously almost absent in the earth's crust and now, if put all together, capable of covering the entire United States with a film.
The life activities of this species we all know well have been specializing on the use of combustion, which, in principle, can be considered as another form of respiration, that is, one that can combine oxygen and carbon. All their production activities ultimately release carbon dioxide into the planet's atmosphere. At this point we have several scenarios. If the concentration of carbon dioxide, i.e., CO2 , reaches 500 parts per million, the balance of anoxic zones will shift toward the free water surface. The hydrogen sulfide bubbles thus released into the atmosphere will wipe out all oxygen-breathing life forms. The planet will consequently lose a wide variety of life forms in a giant mass extinction. However, hydrogen sulfide-producing Archaea will have the opportunity to expand numerically into the ecological niche previously occupied by oxygen-breathing colonizers. Some forms of hybrid oxygen-using aerobic organisms, such as certain jellyfish, flourish under anoxic conditions. Evolution on the planet will thus continue following a new adaptive path, until the next disequilibrium, specializing in an atmosphere now 90 percent carbon dioxide, until a global greenhouse effect makes Earth unlivable, as happened on Venus.
The anoxia that will develop on Earth will be nothing more than a response mechanism of planetary dynamics, which will be triggered when the 500 ppm threshold is reached. We are reaching this threshold. What will be done to prevent humans from pushing the concentration toward this threshold with their CO2 emissions? Unfortunately, we already know the answer: nothing. Try asking all the broadcast television weather broadcasts that tell us on a daily basis how much the concentration of carbon dioxide in the atmosphere corresponds to on a planetary scale: they already provide us with so much data relatively to daily temperatures, why is this parameter hidden from the population?
Monitoring this rate is an extremely important index for our survival on the planet. But sometimes it is better not to know, if every action is carried out in the name of the god money and not in the interests of communities. Our fate is probably already sealed in the great book of cyclical species extinctions, but, if we wish, we can meagerly console ourselves by noting how evolution does not inherently favor some form of life like ours based o n breathing free oxygen or using carbon or water, but how much instead it makes bricolage out of everything it finds. Presumably our Galaxy, like the entire Universe, is overflowing with planets with unimaginable life forms that have adapted and evolved under the most unimaginable conditions that not even the most imaginative of science fiction writers versed in biochemistry, such as Isaac Asimov, was ever able to imagine.
