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Recovery of 16S ribosomal RNA gene fragments from ancient halite

Nature volume 417, pages 432–436 (2002)Cite this article

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.

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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.

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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.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, University of Leicester, Leicester, LE1 9HN, UK

    Steven A. Fish & William D. Grant

  2. British Geological Survey, Keyworth, NG12 5GG, Nottingham, UK

    Thomas J. Shepherd

  3. Department of Biological Sciences, University of Essex, Colchester, CO4 3SQ, Essex, UK

    Terry J. McGenity

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Correspondence to William D. Grant.

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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

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