The three domains were introduced in 1977. They divide cellular life into Archaea, Bacteria and Eukarya domains. Originally the prokaryotes were together, but eubacteria and archaebacterial were later found to be different and split into two groups. Archaea is known to be some of the oldest species of organisms on earth. Archaea and bacteria are similar because they are both prokaryotic, but only bacteria contains peptidoglycan in their cell walls. Most bacteria are pathogenic. Similar to the bacteria, Eukarya can also be pathogenic. Throughout the last two decades there has been a great deal of research that shows much more information, which has subsequently helped classify the organisms into many kingdoms. Archaea is separated from the other two domains because they have membranes composed of branched hydrocarbon chains. 
This chart shows the different characteristics that can be found in each Domain. Some of the characteristics overlap in each Domain. However, there are subtle differences between these Domains that make them unique. Domain is on the top of the taxonomy tree. It is the most broad category an organism can be sorted into. For example, domain Eukarya is clearly different from the other domains because Eukarya includes eukaryotes, multicellular organisms, and sexual reproduction. In addition, the only domains Bacteria and Archaea consist of are organisms that are lithotrophs. The domains Bacteria, Archaea and kingdom Protista from domain Eukarya, are all motile, using the same method for movement, using flagella and cilia to help move. There is only one kingdom from the domain Eukarya, the kingdom Animalia that has a nervous system present. A big difference that makes Archaea unique is that it has linkages, the cell wall lacks peptidoglycan, and they are extremophiles.
Unity and Diversity
All the organisms that live are linked in some way, however what makes them different is linked to their diversity. The diversity was caused by time passing by and evolution taking its course. Even with two different organism looking nothing alike, they still have similar characteristics because theyall came from one organism that evolved over time.
Figure 52: Halobacterium salinarum
Figure 53:Vibrio cholerae
- Unicellular prokaryote
- Gas vesicles
- Flagella for movement
- Cell wall lack peptidoglycan
- Survive harsh environments with harsh conditions - high saline
- Osmoprotectants which helps to equilibrize them with their environment
- If come in contact with water, it can kill the organism
- Captures light to make other chemical matter to make energy- only photoautotroph in Archaea
- Asexual-budding- fast because very simple 
- Bacteria- derives from Archaea
- Unicellular prokaryote
- Gas vesicles
- Flagella for movement
- Synthesize more flagella sometimes depending on circumstances- more complex than just having one, needed because of evolution
- Cell wall containing peptidoglycan, adding to the make up- helped with evolution
- Metabolize both ways, fermentative and oxidative metabolism- slightly more complex being able to do two ways
- Require salt or water to grow, and multiply- asexual
- Heterotrophic, organotrophs
- Pathogen- produces cholera toxin, infecting humans and causing harm to them (main symptom- Diarrhea) 
As you can see, the Bacteria has evolved from the Archaea. The Archaea was very uncomplicated, with only simple characteristics and processes. Another thing that makes the Halobacterium salinarum be a part of the Archaea is its ability to live in the high concentrations of salt. As time went on and the world evolved, areas became less harsh than others. For example, the Vibrio cholera lives in salty environments but not harsh ones like the Archaea. Another big difference is that the cell wall of the Vibrio cholera contains peptidoglycan. This is because of constant evolution in different areas of world. However, most of the charactersitcs are similar because Bacteria directly evolved from Archaea.
Figure 54: E. coli
Figure 55: Paramecium caudatum
E. coli is found in the Domain Bacteria. The Paramecium caudatum is found in the Domain Eukarya, in the kingdom Protista. E. Coli is a unicellular prokaryote. The Paramecium caudatum is also unicellular, however it is a eukaryote. Eukaryotes are thought to have derived from the prokaryotes. In short, the eukaryote is a complex prokaryote because of the nucleus and all the organelles it contains such as the macronucleus, contractile vacuole, and the micronuclei. The E. Coli is an organotroph, consuming organic compounds for a source of energy. It can be found in foods and drinks but also in the humans body, eating away at it, causing many problems for the human.  The Paramecium caudatum is a heterotroph, digesting organic material to make energy. The organism has a food vacuole where bacteria and fluid will be held and where digestion happens.  Even though they both consume the organic substances, the Paramecium caudatum has a complex way of doing it, consisting of a oral cavity to take in large substances and a food vacuole to store it. Other substances are taken in and out of the organism by diffusion for both the organisms. Both these organisms use the same motility. A flagella and cilia around the surface of the organism help it move through the fluid or in the water. Lastly, the E. Coli reproduces asexually via binary fission. This process helps them multiply quickly and efficiently.  The Paramecium caudatum reproduces sexually via conjunction. Conjunction is the most simple sexual process. Because of evolution, the organism found new ways for reproduction especially because of the complexity of the eukaryotic cell. In conclusion, the E. coli and the Paramecium caudatum are very similar. One reason is that the Protist did not evolve long after the Bacteria. The characteristics between these two organisms are very alike. Just some of the characteristics of the Paramecium caudatum have evolved and have became more complex. For example, the eukaryotic cell is complex compared to the prokaryotic cell, and has organelles that help with the complexity of the organism.
Click on one of the Domain buttons below to learn about an individual Domain and organisms that would be classified in it.