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Molecular Phylogeny
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©2000 Gary Olsen, University of Illinois

Major Groups within the Archaea

The major physiological groups within the Archaea (informally, archaes) are extreme thermophiles (including thermoacidophiles), sulfate reducers, methanogens, and extreme halophiles. These physiological groups do not correspond to the phylogenetic groups. This is largely because the methanogens have given rise to multiple other groups, including the halophiles, the sulfate reducers, and at least two other lineages of nonmethanogenic thermophiles.

The thermophilic members of the Archaea include the most thermophilic organisms cultivated in the laboratory, some having optimal growth at > 100 °C. The aerobic thermophiles are also acidophilic; they oxidize sulfur in their environment to sulfuric acid, creating acid hot springs. The hot acidic waters can dissolve limestone and some other minerals out of the surrounding rock matrix, creating boiling mud pots of the insoluble residue from the rock.

The extreme halophiles include the most salt tolerant organisms known. They are aerobic or microaerophilic. They have also invented a form of photosynthesis that does not use chlorophyll.

The sulfate-reducing Archaea are now known to be a wide spread group. One of the reasons that this group has received attention is that sulfate-reducing organisms are responsible for "souring" oil wells (increasing their sulfur content). In addition to increasing the sulfur emissions when the oil is burned (or increasing the cost of refining it), sulfide attacks the metal in well casings and pipelines.

Methanogens are strict anaerobes, yet they gave rise to at least two separate aerobic groups: the halophiles and a thermoacidophilic lineage. Methanogens produce most of the methane in the Earth's atmosphere. Methane is a significant green-house gas (i.e., it is a cause of global warming). Much of this methane production is associated with activities for which humans are at least partially responsible. This includes the flooding of rice paddies and the raising of domestic cattle.

The Archaea Are Prokaryotes in Morphology, But ...

The Archaea are not eukaryotes, which makes them prokaryotes. However, the fact that they are related to Eucarya, not to the other prokaryotic organisms (the Bacteria), means that prokaryotes are not a natural group.23 This is difficult to fully appreciate, since we tend to accord a special status to eukaryotic cells. It is perhaps most easily understood by considering the ability to learn about one group from another:

If we wonder about a biosynthetic reaction in a eukaryote, it makes more sense to use a member of the Archaea as a model than to use a member of the Bacteria. Even though much more money is being spent on analysis of eukaryotic genomes than prokaryotic genomes, due to their smaller size, some prokaryotic genomes will be completed first. Of these, it appears that we will learn more about human genes from the archaeal genomes than from the bacterial genomes.

If we wonder about transcription initiation in Thermococcus celer (an archaeon), should we look at what is known about transcription in E. coli (another prokaryote) or in yeast (a eukaryote)? It is now known that the transcription apparatus of T. celer seems to be much more similar to that of yeast than to that of E. coli.

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