The Nanoarchaeota, proposed as the fourth sub-division of the Archaea in 2002, are known from a single isolate, Nanoarchaeum equitans, which exists in a symbiotic association with the hyperthermophilic Crenarchaeote, Ignicoccus. N. equitans fails to amplify with standard archaeal 16S PCR primers and can only be amplified using specifically designed primers. We have designed a new set of universal archaeal primers that amplify the 16S rRNA gene of all four archaeal sub-divisions, and present two new sets of Nanoarchaeota-specific primers based on all known nanoarchaeal 16S rRNA gene sequences. These primers can be used to detect N. equitans and have generated nanoarchaeal amplicons from community DNA extracted from Chinese, New Zealand, Chilean and Tibetan hydrothermal sites. Sequence analysis indicates that these environments harbour novel nanoarchaeal phylotypes, which, however, do not cluster into clear phylogeographical clades. Mesophilic hypersaline environments from Inner Mongolia and South Africa were analysed using the nanoarchaeal-specific primers and found to contain a number of nanoarchaeal phylotypes. These results suggest that nanoarchaeotes are not strictly hyperthermophilic organisms, are not restricted to hyperthermophilic hosts and may be found in a large range of environmental conditions.
Nanoarchaeaota 16S rRNA Phylogeny Primer Hyperthermophilic Hypersaline
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Chinese, Tibet and Inner Mongolian sediment samples were obtained under the auspices of the joint Chinese-EU-SA MGATech project (QLRT-2001-01972). Chilean sediment samples were obtained by Dr. J. Blamey. GCB was supported by the Royal Society/NRF Program. NG and AC were supported by the NRF HBU-RDP Program. DNA sequencing was conducted by Di James at the University of Cape Town Sequencing Facility and Inqaba Biotech, South Africa. We would like to thank H. Huber for supplying “N. equitans” genomic DNA.
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