Prokaryotes were originally under one domain: Bacteria. They originally were categorized under the Monera kingdom. However, in 1977, Carl Woese, a microbiologist and physicist discovered significant differences between some of the prokaryotes. These differences were so significant that the prokaryotes were separated into two separate domains: Archaea and Bacteria, and hence two kingdoms: Archaea and Eubacteria. Some texts still refer to the Archaea kingdom as the Archaebacteria kingdom; however, this term has recently been abandoned because they are not bacteria; they are archaea.
What makes these two groups of organisms so different is their genetic make-up, primarily the gene sequences of ribosomal RNA (rRNA). Woese found that archaean biochemistry was more similar to that of eukaryotes—multi-celled organisms—than that of eubacteria. In particular, there were similarities with the enzymes involved with transcription and translation of DNA and with several metabolic pathways. The cell membrane of archaea is also unique from that of eubacteria, possessing unusual lipids. Amongst this significant genetic difference, there are many other differences between these two groups of organisms.
Archaea. Archaea ("ancient") microbes are believed to be the ancestors of the protists and the first eukaryotes, due to their genetic make-up. They obtain most of their energy from sulfur, salt, hydrogen, and carbon dioxide. They tend to be more tolerant of extreme environmental conditions and are often found where most other life is unable to exist—such as at the bottom of the sea or in volcanoes.
There are three main types of archaea. The methanogens are anaerobic, meaning they are intolerant of oxygenated areas and produce methane gas. They thrive in swamps, mud, carcasses of animals, and even your intestines! Halophiles ("salt lovers") live in high salt concentrations of water, like the Dead Sea in the Middle East or the Great Salt Lake in Utah. Bacteria can't normally survive in salty environments, but these archaea thrive in it. Then there are thermoacidophiles ("heat lovers"), which live in hot, acidic, sulfuric, areas. Thermoacidophiles can survive temperatures as high as 230 degrees Fahrenheit and pH levels below 2 (hydrochloric acid has a pH of 1). The ability of archaea to survive in extreme environments gave them the name extremophiles.
Recent studies have also found archaea in a broader range of habitats, including soils, oceans, and marshlands. They play an important role as decomposers, helping in the carbon, sulfur, and nitrogen cycles.
Some archaea have been known to have symbiotic relationships like that of mutualism—a partnership between two organisms, in which both organisms benefit from each other—and commensalism—when one organism benefits and the other organism receives neither harm nor gain. As mentioned, archaea are also helpful in biogeochemical cycles, recycling vital elements like nitrogen, carbon, and sulfur. In biotechnology efforts, archaea produce biogas for the treatment of sewage. Archaea also contribute to pollution and global warming. Methane gas is a main source of greenhouse gases, and methanogens are the number one producers of it.
Eubacteria. Eubacteria are probably more commonly known because they thrive in a wider variety of environments. These are bacteria you will most likely find in your body, in your food, or in your home. Most eubacteria live as decomposers and heterotrophs—dependent on others for food. Most decomposers provide an ecological service, as they break down nutrients in dead carcasses, releasing nutrients back into the soil. Cyanobacteria are a type of eubacteria that you may have heard about. It grew in the oceans over 3 billion years ago and was responsible for adding oxygen into our developing atmosphere. So, similar to archaea, eubacteria are also part of biogeochemical cycles. They also help in biotechnology efforts with the treatment of sewage and production of yogurt and cheese.
Clostridium botulina are decomposers that act fast on some food items, releasing a powerful poison. If you ingest these bacteria, you are most likely to get food poisoning. Some heterotrophic eubacteria are pathogens, or disease-causing germs that harm other organisms. In humans, pathogens cause infectious diseases like cholera, syphilis, and tuberculosis—a fatal disease. Some other eubacteria are mutualistic. For example, Escherichia coli, or E. coli, are a type of eubacteria that live inside our colon. They help absorb water and break down vitamins. In return, these bacteria are provided with a comfortable environment and a consistent supply of nutrients by us.
Other common groups of eubacteria are autotrophs—bacteria that can make their own food through photosynthesis. They have a chain-like structure and are commonly found in moist areas like lakes and ponds. Autotrophs indicate that eubacteria are ancestors of plants. There are also chemoautotrophs—bacteria that get their energy from chemical compounds.
When the environment isn't supportive, some eubacteria have the ability to form spores and "hibernate"—in other words, they become metabolically inactive until conditions improve. As lightweight spores, they are able to float in the air and move all over. Within their specific environments, some are immobile while others have flagella that move them along.
Identification. Besides classifying archaea and eubacteria by habitat and means of existence, they are also identified by other means. Identifying an organism as an archaean is mainly done by studying its genetic make-up. Differences in rRNA remain the main classification characteristic. But other characteristics are also considered: