Phylogenetic and Ecological Perspectives on Uncultured Crenarchaeota and Korarchaeota
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Phylogenetic and Ecological Perspectives on Uncultured Crenarchaeota and Korarchaeota SCOTT C. DAWSON, EDWARD F. DELONG AND NORMAN R. PACE
Introduction Molecular phylogenetic analyses divide the domain Archaea into two lineages: Euryarchaeota and Crenarchaeota. Potentially a third main line, Korarchaeota (Woese et al., 1990; Barns et al., 1996), is indicated by only a few environmental sequences and so remains to be further documented. In the late 1970s, at the time of the initial recognition of Archaea as a third domain of life separate from Bacteria or Eucarya, the clade Archaea was thought to consist mostly of “extremeophiles,” organisms inhabiting hostile or unusual settings such as geothermal or hypersaline environments. This perception, which proved to be highly distorted, was founded in the fact that most of the cultivated representatives of Archaea derived from such environments. The diverse physiologies of the cultured examples of Archaea seemed to reflect their settings. Cultured types of Euryarchaeota are physiologically varied, including methanogens, halophiles, and thermophiles. Cultivated members of the Crenarchaeota, on the other hand, have seemed more phenotypically homogeneous. Essentially all cultured Crenarchaeota are sulfur-dependent thermophiles and hyperthermophiles. More recently it has become evident that the cultured organisms represent a minority of crenarchaeal diversity, only one of several phylogenetic groups of Crenarchaeota. The uncultured kinds of organisms have only been encountered through environmental sequence studies. Considering the environmental settings of the uncultured organisms, the majority of types of Crenarchaeota are not thermophiles or “extremophiles” but rather must be viewed as mesophiles or psychrophiles of uncertain physiology. Our new understanding of the diversity of Crenarchaeota is due largely to the use of molecular techniques that survey microbial diversity in natural environments without the traditional requirement to pure-culture microorganisms in order to identify them. These molecular techniques mainly use cloning and sequencing rRNA genes from environmental DNA in order to identify the phylogenetic types of organisms, the
“phylotypes,” that comprise the ecosystem analyzed. Since 1992 (DeLong, 1992), environmental crenarchaeal rDNAs have been encountered in such “mundane” temperate settings as the open ocean, terrestrial soils, and freshwater and marine sediments. In addition to the cosmopolitan, non-thermophilic representatives of Crenarchaeota, rRNA sequences have revealed novel thermophilic lineages in geothermal environments around the world, some related specifically to the novel mesophiles. The applications of molecular methods have expanded spectacularly our view of crenarchaeal diversity. The abundance and wide distribution of Crenarchaeota in the environment attest that they play important, still unknown roles in the global
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