<P> Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure . The particular RNA molecule sequenced, known as 16S rRNA, is present in all organisms and always has the same vital function: the production of proteins . Because this function is so central to life, organisms with mutations of their 16S rRNA are unlikely to survive, leading to great stability in the structure of this nucleotide over many generations . 16S rRNA is also large enough to retain organism - specific information, but small enough to be sequenced in a manageable amount of time . In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that involved splitting the RNA into fragments that could be sorted and compared to other fragments from other organisms . The more similar the patterns between species were, the more closely related the organisms . </P> <P> Woese used his new rRNA comparison method to categorize and contrast different organisms . He sequenced a variety of different species and happened upon a group of methanogens that had vastly different patterns than any known prokaryotes or eukaryotes . These methanogens were much more similar to each other than they were to other organisms sequenced, leading Woese to propose the new domain of Archaea . His experiments showed that the Archaea were more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure . This led to the conclusion that Archaea and Eukarya shared a more recent common ancestor than Eukarya and Bacteria in general . The development of the nucleus occurred after the split between Bacteria and this common ancestor . Although Archaea are prokaryotic, they are more closely related to Eukarya and thus cannot be placed within either the Bacteria or Eukarya domains . </P> <P> One property unique to Archaea is the abundant use of ether - linked lipids in their cell membranes . Ether linkages are more chemically stable than the ester linkages found in Bacteria and Eukarya, which may be a contributing factor to the ability of many Archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity . Comparative analysis of archaeal genomes has also identified several molecular signatures in the form of conserved signature indels and signature proteins which are uniquely present in either all Archaea or different main groups within Archaea . Another unique feature of Archaea is that no other known organisms are capable of methanogenesis (the metabolic production of methane). Methanogenic Archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are Bacteria, as they are often a major source of methane in such environments and can play a role as primary producers . Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas . </P> <P> The relationship between the three domains is of central importance for understanding the origin of life . Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya . Within prokaryotes, archaeal cell structure is most similar to that of gram - positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition . In some phylogenetic trees based upon different gene / protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram - positive bacteria . Archaea and gram - positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I; however, the phylogeny of these genes was interpreted to reveal interdomain gene transfer, and might not reflect the organismal relationship (s). </P>

Where are bacterial members of the domain archaea found