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Extremophiles

, Volume 12, Issue 5, pp 651–656 | Cite as

Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments

  • Ana Casanueva
  • Ncebakazi Galada
  • Gillian C. Baker
  • William D. Grant
  • Shaun Heaphy
  • Brian Jones
  • Ma Yanhe
  • Antonio Ventosa
  • Jenny Blamey
  • Don A. CowanEmail author
Original Paper

Abstract

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.

Keywords

Nanoarchaeaota 16S rRNA Phylogeny Primer Hyperthermophilic Hypersaline 

Notes

Acknowledgments

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.

References

  1. Baker GC, Cowan DA (2004) 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem Soc Trans 32:218–221PubMedCrossRefGoogle Scholar
  2. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555PubMedCrossRefGoogle Scholar
  3. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188–9193PubMedCrossRefGoogle Scholar
  4. Brochier C, Forterre P, Gribaldo S (2005) An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol Biol 5:36PubMedCrossRefGoogle Scholar
  5. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeaota. Nat Rev Microbiol 6:245–252PubMedCrossRefGoogle Scholar
  6. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287PubMedCrossRefGoogle Scholar
  7. Galtier N, Gouy M, Gautier C (1996) Seaview and phylo_win: two graphical tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543PubMedGoogle Scholar
  8. Hohn MJ, Hedlund BP, Huber H (2002) Detection of 16S rDNA sequences representing the novel phylum “Nanoarchaeota”: Indication for a wide distribution in high temperature biotopes. Syst Appl Microbiol 25:551–554PubMedCrossRefGoogle Scholar
  9. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nano-sized hyperthermophilic symbiont. Nature 417:63–67PubMedCrossRefGoogle Scholar
  10. Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stteter KO, Rachel R, Huber H (2008) Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique intimate association of two Archaea. J Bact 190:1743–1750PubMedCrossRefGoogle Scholar
  11. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  12. McCliment EA, Voglesonger KM, O’Day PA, Dunn EE, Holloway JR, Cary SC (2006) Colonization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage. Environ Microbiol 8:114–125PubMedCrossRefGoogle Scholar
  13. Paper W, Jahn U, Hohn MJ, Kronner M, Näther DJ, Burghardt T, Rachel R, Stetter KO, Huber H (2007) Ignicoccus hospitalis sp. nov., the host of “Nanoarchaeum equitans”. Int J Syst Evol Microbiol 57:803–808PubMedCrossRefGoogle Scholar
  14. Stach JEM, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rDNA sequence diversity in soil obtained using different isolation and purification methods. FEMS Microbiol Ecol 36:139–151PubMedCrossRefGoogle Scholar
  15. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustalx windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  16. Waters E, Hohn MJ, Ahel I, Graham DF, Adams MD, Barnstead M et al (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA 100:12984–12988PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2008

Authors and Affiliations

  • Ana Casanueva
    • 1
  • Ncebakazi Galada
    • 1
  • Gillian C. Baker
    • 2
  • William D. Grant
    • 3
  • Shaun Heaphy
    • 3
  • Brian Jones
    • 4
  • Ma Yanhe
    • 5
  • Antonio Ventosa
    • 6
  • Jenny Blamey
    • 7
  • Don A. Cowan
    • 1
    Email author
  1. 1.Department of Biotechnology, Institute for Microbial Biotechnology and MetagenomicsUniversity of the Western CapeBellvilleSouth Africa
  2. 2.Department of Biodiversity and Conservation BiologyUniversity of the Western CapeBellvilleSouth Africa
  3. 3.Department of Microbiology and ImmunologyUniversity of LeicesterLeicesterUK
  4. 4.Genencor InternationalLeidenThe Netherlands
  5. 5.Institute of Microbiology, Chinese Academy of SciencesBeijingChina
  6. 6.Department of Microbiology and ParasitologyUniversity of SevilleSevilleSpain
  7. 7.Fundación BiocienciaSantiagoChile

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