Of the three primary phylogenetic domains--Archaea; (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes)--Archaea is; the least understood in terms of its diversity, physiologies, and ecological; panorama. Although many species of Crenarchaeota (one of the two recognized; archaeal kingdoms sensu Woese [Woese, C. R., Kandler, O. & Wheelis, M. L.; (1990) Proc. Natl. Acad. Sci. USA 87, 4576-4579]) have been isolated, they; constitute a relatively tight-knit cluster of lineages in phylogenetic analyses; of rRNA sequences. It seemed possible that this limited diversity is merely; apparent and reflects only a failure to culture organisms, not their absence. We; report here phylogenetic characterization of many archaeal small subunit rRNA; gene sequences obtained by polymerase chain reaction amplification of mixed; population DNA extracted directly from sediment of a hot spring in Yellowstone; National Park. This approach obviates the need for cultivation to identify; organisms. The analyses document the existence not only of species belonging to; well-characterized crenarchaeal genera or families but also of crenarchaeal; species for which no close relatives have so far been found. The large number of; distinct archaeal sequence types retrieved from this single hot spring was; unexpected and demonstrates that Crenarchaeota is a much more diverse group than; was previously suspected. The results have impact on our concepts of the; phylogenetic organization of Archaea.
