Extraction of DNA from Acidic, Hydrothermally Modified Volcanic Soils

Ruth M. Henneberger; Malcolm R. Walter; Roberto P. Anitori

doi:10.1071/EN06013

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Extraction of DNA from Acidic, Hydrothermally Modified Volcanic Soils

Ruth M. Henneberger ^A ^B , Malcolm R. Walter ^A ^B ^C and Roberto P. Anitori ^A ^B ^D ^E

+ Author Affiliations

- Author Affiliations

^A Australian Centre for Astrobiology, Macquarie University Biotechnology Research Institute, Macquarie University, North Ryde, NSW 2109, Australia.

^B Macquarie University Biotechnology Research Institute, Macquarie University, North Ryde, NSW 2109, Australia.

^C Department of Earth and Planetary Sciences, Macquarie University, North Ryde, NSW 2109, Australia.

^D Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.

^E Corresponding author. Email: ranitori@rna.bio.mq.edu.au

Environmental Chemistry 3(2) 100-104 https://doi.org/10.1071/EN06013
Submitted: 15 February 2006 Accepted: 24 March 2006 Published: 5 May 2006

Environmental Context. Microorganisms are intimately involved in geochemical processes. For example, they are major players in the environmental cycling of important elements (e.g. carbon, sulfur, nitrogen, iron), rock weathering, and the formation of ores and petroleum. Identification of the environmental microbiota, commonly achieved via DNA techniques, is essential for an understanding of these processes. The main focus of this Rapid Communication is to demonstrate that endogenous DNA can be extracted from acidic, volcanic soil samples.

Abstract. Acidic soils for microbial diversity studies were collected from Devil’s Kitchen, a fumarolic field on Mt Hood, USA. The very dense soils, which contain clay and other minerals, are derived from andesitic and dacitic rocks altered by volcanic heat and acidic, sulfur-rich hydrothermal steam. An initial attempt to extract biomass DNA using a mechanical-based cell lysis protocol was ineffective. However, by using various other protocols, DNA was successfully extracted, leading to the identification of several acidophilic Mt Hood extremophiles. The results emphasise the importance of testing different extraction procedures when dealing with apparently intractable samples.

Keywords. : DNA extraction — microbes — Mt Hood — soils

Acknowledgments

RMH was funded by Macquarie University (Postgraduate Research Fund and an International Travel Scholarship). We are grateful to Prof. Peter Bergquist for advice and manuscript editing, and Dana Rogoff, Tom Bennett, Dr Steve Boyer, Bob McGown for assistance during sample collection. Tin Tin Win for XRD analyses. Paul Norman and the USDA Forest Service for the Mt Hood sampling permit. Debra Birch for microscopy. Florian Selch for assistance in the identification of cultured microbes.

References

Extraction of DNA from Acidic, Hydrothermally Modified Volcanic Soils

Acknowledgments

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