Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Recovery of 16S ribosomal RNA gene fragments from ancient halite

A Corrigendum to this article was published on 14 November 2002

Abstract

During the last decade, sensitive techniques for detecting DNA have been successfully applied to archaeological and other samples that were a few hundred to a few thousand years old1,2. Nevertheless, there is still controversy and doubt over claims of exceptionally ancient DNA3. Additional accounts stretching back nearly a century suggest that microorganisms may survive over geological time in evaporite deposits4,5. There is, however, often doubt over the age relationship between evaporite formation and the incorporation of microorganisms6. Here, we have used petrographic and geochemical techniques (laser ablation microprobe–inductively coupled plasma–mass spectrometry) to verify the estimated geological age of halite (NaCl) evaporite samples. Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). Haloarchaeal 16S rDNA amplicons were present in one sample (11–16 Myr), whereas other samples (65–425 Myr) yielded only bacterial 16S rDNA amplicons. Terminal restriction fragment length polymorphism analyses indicate complex and different populations of microorganisms or their free DNA in ancient halites of different ages.

Your institute does not have access to this article

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Photomicrograph of a typical chevron halite (taken in transmitted light) showing well developed growth zones parallel to the cube faces decorated with thousands of microscopic, cuboid brine inclusions.
Figure 2: Sizing and visualization by agarose gel electrophoresis of amplified DNA from nested PCR using primers 27Fa/1524Ra in the first round of amplification (lanes a–h) and 353Fa/1392Ru in the second round (lanes i–p).
Figure 3: t-RFLP analysis of quality controlled Poland (a, c) and Thailand (b, d) PCR products generated using FAM-labelled primer FD3 and 1392 Ru.
Figure 4: Phylogenetic trees of halobacterial (a) and bacterial (b) 16S rRNA genes obtained from ancient halite samples from Poland, Thailand and Michigan prepared from quality controlled and non-quality controlled material.

References

  1. Woodward, S. R., Weyand, N. J. & Bunnell, M. DNA sequence from Cretaceous period bone fragments. Science 266, 1229–1232 (1994)

    ADS  CAS  Article  Google Scholar 

  2. Cano, R., Poinar, H. N. & Poinar, G. O. Isolation and partial characterisation of DNA from the bee Proplebeia dominicans (Apidae: Hymenoptera) in 25–40 million year old Dominican amber. Med. Sci. Res. 20, 249–251 (1992)

    CAS  Google Scholar 

  3. Smith, A. & Austin, J. J. Can geologically ancient DNA be recovered from the fossil record? Geoscientist 7, 8–11 (1998)

    Google Scholar 

  4. McGenity, T. J., Gemmell, R. T., Grant, W. D. & Stan-Lotter, H. Origins of halophilic microorganisms in ancient salt deposits. Environ. Microbiol. 2, 243–250 (2000)

    CAS  Article  Google Scholar 

  5. Vreeland, R. H., Rosenzweig, W. D. & Powers, D. W. Isolation of a 250 million year old halotolerant bacterium from a primary salt crystal. Nature 407, 897–899 (2000)

    ADS  CAS  Article  Google Scholar 

  6. Hazen, R. M. & Roedder, E. How old are bacteria from the Permian age? Nature 411, 155 (2001)

    ADS  CAS  Article  Google Scholar 

  7. Norton, C. F. & Grant, W. D. Survival of halobacteria within fluid inclusions in salt crystals. J. Gen. Microbiol. 134, 1365–1373 (1988)

    Google Scholar 

  8. Gemmell, R. T., McGenity, T. J. & Grant, W. D. Use of molecular techniques to investigate possible long term dormancy of halobacteria in ancient salt deposits. Ancient Biomol. 2, 125–133 (1998)

    CAS  Google Scholar 

  9. Wardlow, N. C. & Schwerdtner, W. M. Halite-anhydrite seasonal layers in the Middle Devonian Prairie Formation, Saskatchewan, Canada. Geol. Soc. Am. Bull. 77, 331–342 (1966)

    ADS  Article  Google Scholar 

  10. Roedder, E. The fluids in salt. Am. Mineral. 69, 413–439 (1984)

    CAS  MATH  Google Scholar 

  11. Shepherd, T. J., Ayora, C., Cendón, D. I., Chenery, S. R. & Moissette, A. Quantitative solute analysis of single fluid inclusions in halite by LA-ICP-MS and cryo-SEM-EDS: complementary microbeam techniques. J. Eur. Mineral. 10, 1097–1108 (1998)

    CAS  Article  Google Scholar 

  12. Gunther, D., Audetat, A., Frischknecht, R. & Heinrich, C. A. Quantitative analysis of major, minor and trace elements in fluid inclusions using laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS). J. Anal. At. Spectrom. 13, 263–270 (1998)

    CAS  Article  Google Scholar 

  13. Timofeeff, M. N., Lowenstein, T. K. & Hardie, L. A. in Ninth Ann. V.M. Goldschmidt Conf. 299 (abstract) (Lunar and Planetary Institute, Houston, 1999)

    Google Scholar 

  14. Hardie, L. A. Evaporites, marine or non-marine? Am. J. Sci. 284, 193–240 (1984)

    ADS  CAS  Article  Google Scholar 

  15. Hardie, L. A. Secular variations in seawater chemistry: an explanation for the coupled secular variation in the mineralogies of marine limestone and potash evaporites over the past 600 my. Geology 24, 279–283 (1996)

    ADS  CAS  Article  Google Scholar 

  16. Zimmermann, H. On the origin of fluids included in Phanerozoic marine halite; basic interpretation strategies. Geochim. Cosmochim. Acta 65, 35–45 (2001)

    ADS  CAS  Article  Google Scholar 

  17. Timofeeff, M. N., Lowenstein, T. K. & Blackburn, W. H. ESEM-EDS. An improved technique for major element chemical analysis of fluid inclusions. Chem. Geol. 164, 171–182 (2000)

    ADS  CAS  Article  Google Scholar 

  18. Timofeeff, M. N. et al. Evaluating seawater chemistry from fluid inclusions in halite: examples from modern marine and non-marine environments. Geochim. Cosmochim. Acta 65, 2293–2300 (2001)

    ADS  CAS  Article  Google Scholar 

  19. Rosler, H. J. & Lange, H. Geochemical Tables—Table 97: Composition of sea water (Elsevier, Amsterdam/London/New York, 1972)

    Google Scholar 

  20. Sommers, R. & Tautz, D. Minimal homology requirements for PCR primers. Nucleic Acids Res. 17, 674 (1989)

    Google Scholar 

  21. Rychlik, W. Priming efficiency in PCR. Biotechniques 18, 84–89 (1995)

    CAS  PubMed  Google Scholar 

  22. Rychlik, W., Spencer, W. J. & Rhoads, R. E. Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res. 18, 6409–6412 (1990)

    CAS  Article  Google Scholar 

  23. Kalmbach, S., Manz, W., Wecke, J. & Szewzyk, U. Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov., and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. Int. J. Syst. Bacteriol. 49, 769–777 (1999)

    Article  Google Scholar 

  24. Müller, A. & Schwartz, W. Über das Vorkommen von Mikroorganismen in Salzlagerstätten (geomikrobiologische Untersuchungen III). Zeitschrift Deutschen Geologischen Gesellschaft 105, 789–802 (1953)

    Google Scholar 

  25. Norton, C. F., McGenity, T. J. & Grant, W. D. Archaeal halophiles (halobacteria) from two British salt mines. J. Gen. Microbiol. 139, 1077–1081 (1993)

    CAS  Article  Google Scholar 

  26. Grant, W. D., Gemmell, R. T. & McGenity, T. J. Halobacteria: the evidence for longevity. Extremophiles 2, 279–287 (1998)

    CAS  Article  Google Scholar 

  27. Höss, M. & Pääbo, S. DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res. 21, 3913–3914 (1993)

    Article  Google Scholar 

  28. Jukes, T. H. & Cantor, C. R. in Mammalian Protein Metabolism (ed. Munro, H. N.) Vol. 3, 21–132 (Academic, New York, 1969)

    Book  Google Scholar 

  29. Saitou, N. & Nei, M. The neighbour-joining method: a new approach for constructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The samples were provided by M. N. Timofeef, S. Brennan and T. K. Lowenstein, and we acknowledge their contribution to the research. We also thank D. Gunther and B. Hattendorf for undertaking corroborative chemical analysis of the brine inclusions. This work was supported by an NERC grant.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to William D. Grant.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fish, S., Shepherd, T., McGenity, T. et al. Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417, 432–436 (2002). https://doi.org/10.1038/417432a

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/417432a

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing