Archaea

environment by decomposing organic matter. Some of these are toxic to humans but are responsible for making many kinds of antibiotics. These are eukaryotic cells and include yeasts, mushrooms, and molds. Oxygen is necessary for metabolism. They get nutrients via absorption and will undergo sexual or asexual reproduction through spore formation.

• Plantae—these are the part of the life cycle that undergoes photosynthesis and include many different species, including seed-bearing plants and non-seedbearing plants, flowering and nonflowering plants, and vascular and nonvascular plants. We will talk more about plants in a subsequent chapter.

• Animalia—this is the animal kingdom. They are eukaryotic and, while most are aquatic, there are many land animals. They depend on plants and other animals for nutrition. Most will reproduce via sexual reproduction, which involves male and female gametes that are fertilized. Fish, insects, mammals, amphibians, sponges, and worms belong to this category. All require oxygen for metabolism.

They acquire nutrients via ingestion. A few will undergo asexual reproduction as part of their life cycle.

ARCHAEA

In this section, we’ll talk about archaea as a domain because it hasn’t been discussed before. These are prokaryotic microbes that have no cell nucleus. Previously considered bacteria, they will have different ribosomal RNA and other different features that make them unique among species. There is just one kingdom, called the Archaebacteria and multiple phyla. As you will see, they share genes similar to eukaryotes as well, particularly those involved in the enzymatic control of transcription and translation.

While considered extreme organisms, they are also found in more traditional environments, such as marshlands, soil, oceans, and in the human mouth, on the human skin, and in the gut. There are many archaea species in the oceans, where they play a role in the nitrogen cycle and the carbon cycle. They can be commensals or mutualists but tend not to be pathogenic. There are several phyla that have been proposed as already mentioned. The Euryarchaeota and Crenarchaeota are well-known

and understood, while several others (such as Korarchaeota, Parvarchaeota, and Micrarchaeota) have been proposed and are less understood.

There is a lot of horizontal gene transfer between organisms, making the classification of species difficult. In addition, some argue there aren’t many practical reasons to separate out many of these species, with the subcategory of phyla being more practical.

As mentioned in the last chapter, life began on earth about 3.8 billion years ago with the identification of biogenic rocks that date from about 3.7 billion years ago. It is possible that a thermophile that was neither an archaea organism or a bacterial organism was the common ancestor to bacteria and archaea species.

Archaea have ether-linked lipids, which differ from the ester-linked lipids in bacteria and eukaryotes. Their cell membranes are made of pseudopeptidoglycan rather than peptidoglycan (in bacterial species). Their chromosomes are circular like bacteria but have transcription and translation enzymes like the eukaryotes. There are no membrane-bound organelles. They have various metabolisms, with methanogenesis being unique to the domain. They reproduce both asexually and through horizontal gene transfer, similar to bacteria.

While Archaea as a domain appear more similar to Bacteria, they are actually closer biochemically to Eukarya because of shared translation and transcription protein systems and because of other biochemical similarities. Recent research suggests that Bacteria probably came first and then Archaea, followed later by Eukarya. As mentioned, their cell membranes are unique, having ether linkages in the cell membranes, making them more stable than that of Bacteria and Eukarya. This is probably why they survive better in extreme environments when other organisms do not survive.

Archaea can be less than 0.1 micrometers in diameter or over 15 micrometers in diameter, with different shapes, such as spherical, rod-shaped, spiral, or plate-shaped. Even needle-shaped and irregular lobe-shaped archaea can be seen, as well as rectangular rod-shaped organisms. Their cytoskeleton and cell walls help to acquire these unique shapes. Some will aggregate or will form filaments, seen also in biofilms. There is a Thermococcus species that fuses together to form single “giant” cells. Another

genus called Pyrodictium form long, hollow tubes, known as cannulae, forming a bushshaped group of organisms.

Almost all of these archaea species will have a cell wall. The cell walls do not consist of peptidoglycan like bacteria but consist of pseudopeptidoglycan, which has its own chemical structure but looks somewhat like bacterial cell walls. These organisms will often have flagellae that act similar to bacteria with their action powered by a proton gradient, just like in bacteria. The composition of the flagella is different than is seen in bacteria. Rather than having a hollow flagellum seen in bacteria, the flagellum is made by adding protein subunits to the base.

As mentioned, the cell membranes of archaea are unique. Remember that phospholipids have a hydrophobic and a hydrophilic end. In most organisms, these are seen as a lipid bilayer, with two lipid sheets connected to one another by the fact that the hydrophobic cores are not separable. The four main ways that the lipid membranes of archaea are unique include the following:

• Ether lipid bonds at the hydrophilic, glycerol end. This makes the bond more stable than in bacteria and eukaryotes.

• The glycerol end is the mirror image of that seen in other organisms. This means they have different enzymes making their cell membrane.

• The lipid tails are different than other organisms with multiple side-branches not seen in other organisms, making them less leaky during high temperatures.

• In some archaea, this membrane is not a lipid bilayer but a lipid monolayer with two polar ends and a hydrophobic interior.

The metabolism of archaea as a domain is somewhat unique to these organisms. Some will be chemotrophs, getting energy from sulfur and ammonia compounds. These include anaerobic methane oxidizing organisms, methanogens, and nitrification organisms. The energy released from these compounds will make ATP energy via the process of chemiosmosis—very similar to that seen in the mitochondria of eukaryotic cells.

There are also phototrophs that use the sun’s light for fixation of carbon, which is not true photosynthesis because they do not make oxygen. These include the Halobacterium species. There are lithotrophs (that gain energy from inorganic compounds) and organotrophs (that gain energy from organic compounds). As mentioned, there are methanogens that make methane gas, which is believed to be one of the earliest forms of metabolism. Acetotrophs are archaea that take acetic acid and break it down into methane gas and carbon dioxide. Others will use CO2 from the atmosphere to fix carbon, using a type of Calvin cycle or reverse Krebs cycle.

As for genetics, they have a circular chromosome like bacteria as well as plasmids, which are of course, independent from the main chromosome. Plasmids can be passed from one organism to another in a process like bacterial conjugation. They have the ability to become infected by dsDNA viruses that have specific and unusual shapes. Up to 15 percent of the proteins on the archaea genome are unique to this domain, such as those that participate in methanogenesis. While the RNA polymerase molecule is unique to the domain, the way that transcription and translation happens is very close to what happens in eukaryotes.

Archaea can reproduce via binary fission, multiple fission, fragmentation, or budding. They do not participate in mitosis or meiosis. The cell cycle is related to both bacterial and eukaryotic cell cycles. Unlike bacteria, however, they have multiple origins of replication using DNA polymerases that are very similar to that seen in eukaryotes. While eukaryotes and bacteria will make spores, this is not true of the archaea. Certain of the Haloarchaea species will switch cell shapes in order to survive in low salt concentrations, these do not represent reproductive structures like spores are.

About 20 percent of the microbes in the ocean are archaea. While the first ones known to man were extremophiles, living in very high temperatures, very low temperatures, and in different chemical environments, they are also “mesophiles”, meaning they live in moderate conditions, such as marshland, oceans, intestinal tracts, soils, and sewage.

The four main extremophiles are thermophiles, acidophiles, alkaliphiles, and halophiles. Some species of archaea belong to more than one group and the organisms of the same phylum do not necessarily share the same extreme environments. There are also