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PCR-based analysis of microbial communities during the EuroGeoMars campaign at Mars Desert Research Station, Utah

Published online by Cambridge University Press:  22 March 2011

Cora S. Thiel ,
Pascale Ehrenfreund ,
Bernard Foing ,
Vladimir Pletser  and
Oliver Ullrich
Cora S. Thiel*
Affiliation:
Institute of Medical Physics and Biophysics,CeNTech, University of Muenster, Heisenbergstrasse 11, D-48149 Muenster, Germany
Pascale Ehrenfreund
Affiliation:
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, NL-2300 RA, Leiden, The Netherlands
Bernard Foing
Affiliation:
Science and Robotic Exploration Directorate, European Space Agency, ESTEC, P.O. Box 299, NL-2200 AG, Noordwijk, The Netherlands
Vladimir Pletser
Affiliation:
Human Space Flight Directorate, European Space Agency, ESTEC, P.O. Box 299, NL-2200 AG, Noordwijk, The Netherlands
Oliver Ullrich
Affiliation:
Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz, D-39106 Magdeburg, Germany Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
*
e-mail: [email protected]
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Abstract

The search for evidence of past or present life on Mars will require the detection of markers that indicate the presence of life. Because deoxyribonucleic acid (DNA) is found in all known living organisms, it is considered to be a ‘biosignature’ of life. The main function of DNA is the long-term storage of genetic information, which is passed on from generation to generation as hereditary material. The Polymerase Chain Reaction (PCR) is a revolutionary technique which allows a single fragment or a small number of fragments of a DNA molecule to be amplified millions of times, making it possible to detect minimal traces of DNA. The compactness of the contemporary PCR instruments makes routine sample analysis possible with a minimum amount of laboratory space. Furthermore the technique is effective, robust and straightforward. Our goal was to establish a routine for the detection of DNA from micro-organisms using the PCR technique during the EuroGeoMars simulation campaign. This took place at the Mars Society's Mars Desert Research Station (MDRS) in Utah in February 2009 (organized with the support of the International Lunar Exploration Working Group (ILEWG), NASA Ames and the European Space Research and Technology Centre (ESTEC)). During the MDRS simulation, we showed that it is possible to establish a minimal molecular biology lab in the habitat for the immediate on-site analysis of samples by PCR after sample collection. Soil and water samples were taken at different locations and soil depths. The sample analysis was started immediately after the crew returned to the habitat laboratory. DNA was isolated from micro-organisms and used as a template for PCR analysis of the highly conserved ribosomal DNA to identify representatives of the different groups of micro-organisms (bacteria, archaea and eukarya). The PCR products were visualized by agarose gel electrophoresis and documented by transillumination and digital imaging. The microbial diversity in the collected samples was analysed with respect to sampling depth and the presence or absence of vegetation. For the first time, we have demonstrated that it is possible to perform direct on-site DNA analysis by PCR at MDRS, a simulated planetary habitat in an extreme environment that serves as a model for preparation and optimization of techniques to be used for future Mars exploration.

Keywords

astrobiologylife detectionMars Desert Research Stationmicrobial communitiesPCR instrumentationribosomal DNA
Type
Research Article
Information
International Journal of Astrobiology , Volume 10 , Special Issue 3: Special issue: Astrobiology field research in Moon/Mars analogue environments , July 2011 , pp. 177 - 190
Copyright
Copyright © Cambridge University Press 2011

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References

Ahram Biosystems (2010). Available online at http://www.ahrambio.com/product.html (accessed 20 October 2010).Google Scholar
Becquerel, P. (1950). La suspension de la vie au dessous de 1/20K absolu par démagnétisation adiabatique de l'alun de fer dans le vide le plus elevé. C. R. Hebd. Séances Acad. Sci. Paris 231, 261–263.Google Scholar
Cary, S.C., McDonald, I.R., Barrett, J.E. & Cowan, D.A. (2010). On the rocks: the microbiology of Antarctic Dry Valley soils. Nat. Rev. Microbiol. 8, 129–138.CrossRefGoogle ScholarPubMed
Cleaves, H.J. II, Jonsson, C.M., Jonsson, C.L., Sverjensky, D.A. & Hazen, R.M. (2010). Adsorption of nucleic acid components on rutile (TiO(2)) surfaces. Astrobiology 10, 311–323.CrossRefGoogle Scholar
Connon, S.A., Lester, E.D., Shafaat, H.S., Obenhuber, D.C. & Ponce, A. (2007). Bacterial diversity in hyperarid Atacama Desert soils. J. Geophys. Res. 112, G04S17.Google Scholar
Córdoba-Jabonero, C., Zorzano, M.P., Selsis, F., Patel, M.R. & Cockell, C.S. (2005). Radiative zones in Martian polar environments. Icarus 175, 360–371.CrossRefGoogle ScholarPubMed
DeLong, E.F. (1992). Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U.S.A. 89, 5685–5689.CrossRefGoogle ScholarPubMed
Direito, S.O.L., Ehrenfreund, P., Marees, A., Staats, M., Foing, B. & Röling, W.F.M. (2011). A wide variety of extremophiles and large beta-diversity at the Mars Desert Research Station (Utah). Int. J. Astrobiol (Special Issue). DOI: 10.1017/S1473550411000012CrossRefGoogle Scholar
Drees, K.P., Neilson, J.W., Betancourt, J.L., Quade, J., Henderson, D.A., Pryor, B.M. & Maier, R.M. (2006). Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Appl. Environ. Microbiol. 72, 7902–7908.CrossRefGoogle ScholarPubMed
Eglinton, G. & Logan, G.A. (1991). Molecular preservation. Philos. Trans. R. Soc. Lond. B 333, 315–327; discussion 27–28.Google ScholarPubMed
Ehrenfreund, P., Foing, B.H., Stoker, C., Zavaleta, J., Quinn, R., Blake, D., Martins, Z., Sephton, M., Becker, L., Orzechowska, G.et al. (2010). EuroGeoMars Field Campaign: Sample Analysis of Organic Matter and Minerals. LPI Contribution No. 41, p. 1723.Google Scholar
Ehrenfreund, P., Röling, W., Thiel, C.S., Quinn, R., Septhon, M., Stoker, C., Direito, S., Kotler, M., Martins, Z., Orzechowska, G.E., Kidd, R. & Foing, B.F. (2011). Astrobiology and habitability studies in preparation for future Mars missions: trends from investigating minerals, organics and biota. Int. Journal of Astrobiology, Special Issue.CrossRefGoogle Scholar
Fajardo-Cavazos, P., Langenhorst, F., Melosh, H.J. & Nicholson, W.L. (2009). Bacterial spores in granite survive hypervelocity launch by spallation: implications for lithopanspermia. Astrobiology 9, 647–657.CrossRefGoogle ScholarPubMed
Fajardo-Cavazos, P., Link, L., Melosh, H.J. & Nicholson, W.L. (2005). Bacillus subtilis spores on artificial meteorites survive hypervelocity atmospheric entry: implications for Lithopanspermia. Astrobiology 5, 726–736.CrossRefGoogle ScholarPubMed
Fajardo-Cavazos, P., Schuerger, A.C. & Nicholson, W.L. (2010). Exposure of DNA and Bacillus subtilis spores to simulated Martian environments: use of quantitative PCR (qPCR) to measure inactivation rates of DNA to function as a template molecule. Astrobiology 10, 403–411.CrossRefGoogle ScholarPubMed
Foing, B. (2009). Summary Report. EuroGeoMars Campaign: Last Rotation Crew 77. End of Rotation Report (online). Available at http://desert.marssociety.org/mdrs/fs08/0227/summary.asp (accessed 1 November 2010).Google Scholar
Foing, B.H., Stoker, C., Zavaleta, J., Ehrenfreund, P., Thiel, C., Sarrazin, P., Blake, D., Page, J., Pletser, V., Hendrikse, J., Direito, S., Kotler, M., Martins, Z., Orzechowska, G., Gross, C., Wendt, L., Clarke, J., Borst, A.M., Peters, S.T.M., Wilhelm, M.-B., Davies, G.R. & ILEWG EuroGeoMars 2009 team (2011). Field Astrobiology Research in Moon-Mars Analogue Site: Instruments & Methods. Int. Journal of Astrobiology, Special Issue.Google Scholar
Foing, B.H., Mahapatra, P., Boche-Sauvan, L., Som, S., Page, J., Stoker, C., Zhavaleta, J., Sarrazin, P., Blake, D., Poulakis, P.et al. (2010). ExoGeoLab Test Bench for Landers, Rovers and Astrobiology. LPI Contribution No. 1538, p. 5477.Google Scholar
Haile, J., Holdaway, R., Oliver, K., Bunce, M., Gilbert, M.T., Nielsen, R., Munch, K., Ho, S.Y., Shapiro, B. & Willerslev, E. (2007). Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol. Biol. Evol. 24, 982–989.CrossRefGoogle ScholarPubMed
Hofreiter, M., Mead, J.I., Martin, P. & Poinar, H.N. (2003). Molecular caving. Curr. Biol. 13, R693–R695.CrossRefGoogle ScholarPubMed
Hofreiter, M., Serre, D., Poinar, H.N., Kuch, M. & Päabo, S. (2001). Ancient DNA. Nat. Rev. Genet. 2, 353–360.CrossRefGoogle ScholarPubMed
Horikawa, D.D., Sakashita, T., Katagiri, C., Watanabe, M., Kikawada, T., Nakahara, Y., Hamada, N., Wada, S., Funayama, T., Higashi, S. et al. (2006). Radiation tolerance in the tardigrade Milnersium tardigradum. Int. J. Radiat. Biol. 82, 843–848.CrossRefGoogle ScholarPubMed
Horneck, G. (2003). Could life travel across interplanetary space? Panspermia revisited. In Evolution on Planet Earth: The Impact of the Physical Environment, ed. Rothschild, L.J. & Lister, A.M., pp. 109–127. London: Academic Press.CrossRefGoogle Scholar
Horneck, G. (2008b). The microbial case for Mars and its implication for human expeditions to Mars. Acta Astronaut. 63, 1015–1024.CrossRefGoogle Scholar
Horneck, G., Stöffler, D., Ott, S., Hornemann, U., Cockell, C.S., Moeller, R., Meyer, C., de Vera, J.P., Fritz, J., Schade, S. et al. (2008a). Microbial rock inhabitants survive hypervelocity impacts on Mars-like host planets: first phase of lithopanspermia experimentally tested. Astrobiology 8, 17–44.CrossRefGoogle ScholarPubMed
Inagaki, F., Okada, H., Tsapin, A.I. & Nealson, K.H. (2005). Microbial survival: the paleome: a sedimentary genetic record of past microbial communities. Astrobiology 5, 141–153.CrossRefGoogle ScholarPubMed
Isenbarger, T.A., Carr, C.E., Johnson, S.S., Finney, M., Church, G.M., Gilbert, W., Zuber, M.T. & Ruvkun, G. (2008). The most conserved genome segments for life detection on Earth and other planets. Orig. Life Evol. Biosph. 38, 517–533.CrossRefGoogle ScholarPubMed
Jönsson, K.I., Rabbow, E., Schill, R.O., Harms-Ringdahl, M. & Rettberg, P. (2008). Tardigrades survive exposure to space in low Earth orbit. Curr. Biol. 18, R729–R731.CrossRefGoogle ScholarPubMed
Lane, D.J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, ed. Stackebrandt, E. & Goodfellow, M., pp. 115–175. Wiley, New York.Google Scholar
Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709–715.CrossRefGoogle ScholarPubMed
Lyon, D.Y., Monier, J.M., Dupraz, S., Freissinet, C., Simonet, P. & Vogel, T.M. (2010). Integrity and biological activity of DNA after UV exposure. Astrobiology 10, 285–292.CrossRefGoogle ScholarPubMed
Moeller, R., Horneck, G., Rabbow, E., Reitz, G., Meyer, C., Hornemann, U. & Stöffler, D. (2008). Role of DNA protection and repair in resistance of Bacillus subtilis spores to ultrahigh shock pressures simulating hypervelocity impacts. Appl. Environ. Microbiol. 74, 6682–6689.CrossRefGoogle ScholarPubMed
Mormile, M.R., Hong, B.Y. & Benison, K.C. (2009). Molecular analysis of the microbial communities of Mars analog lakes in Western Australia. Astrobiology 9, 919–930.CrossRefGoogle ScholarPubMed
Mullis, K.B. & Faloona, F.A. (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155, 335–350.CrossRefGoogle Scholar
Olsson-Francis, K. & Cockell, C.S. (2010). Experimental methods for studying microbial survival in extraterrestrial environments. J. Microbiol. Methods 80, 1–13.CrossRefGoogle ScholarPubMed
Päabo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L. & Hofreiter, M. (2004). Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645–679.CrossRefGoogle ScholarPubMed
Parnell, J., Cullen, D.C., Sims, M.R., Bowden, S., Cockell, C.S., Court, R., Ehrenfreund, P., Gaubert, F., Grant, W., Parro, V. et al. (2007). Searching for life on Mars: selection of molecular targets for ESA's Aurora ExoMars mission. Astrobiology 7, 578–604.CrossRefGoogle ScholarPubMed
Pavlov, A.K., Shelegedina, V.N., Vdovina, M.A. & Pavlov, A.A. (2010). Growth of microorganisms in Martian-like shallow subsurface conditions: laboratory modeling. Int. J. Astrobiol. 9, 51–58.CrossRefGoogle Scholar
Poole, A.M. & Willerslev, E. (2007). Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars? Astrobiology 7, 801–814.CrossRefGoogle ScholarPubMed
Promega (2010). Available online at: http://www.promega.com/maxwell16/ (accessed 20 October 2010).Google Scholar
Qiagen (2010). Available online at: http://www.qiagen.com/products/automation/qiacube.aspx?ShowInfo=1&r=2721 (accessed 20 October 2010).Google Scholar
Rebecchi, L., Altiero, T., Guidetti, R., Cesari, M., Bertolani, R., Negroni, M. & Rizzo, A.M. (2009). Tardigrade resistance to space effects: first results of experiments on the LIFE-TARSE mission on FOTON-M3 (September 2007). Astrobiology 9, 581–591.CrossRefGoogle ScholarPubMed
Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A. & Arnheim, N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.CrossRefGoogle ScholarPubMed
Secosky, J. (2008). Summary of biology studies done at MDRS (online) Available at: http://desert.marssociety.org/research-summary.asp (accessed 20 October 2010).Google Scholar
Sermon, K. & De Rycke, M. (2007). Single cell diagnostics. Methods Mol. Med. 132, 31–42.CrossRefGoogle Scholar
Smith, S.E. & Read, D.J. (1997). Mycorhizal Symbiosis. Academic Press, San Diego, CA.Google Scholar
Thiel, C.S., Pletser, V. & Foing, B. (2011). Human crew related aspects for astrobiology research. Int. J. Astrobiol. Special Issue.CrossRefGoogle Scholar
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C. et al. (2005). Comparative metagenomics of microbial communities. Science 308, 554–557.CrossRefGoogle ScholarPubMed
Van de Peer, Y., Chapelle, S. & de Wachter, R. (1996). A quantitative map of nucleotide substitution rates in bacterial ribosomal subunit RNA. Nucleic Acids Res., 24, 3381–3391.CrossRefGoogle Scholar
Van Rhijn, P. & Vanderleyden, J. (1995). The rhizobia-plant symbiosis. Microbiol. Rev. 59, 124–142.CrossRefGoogle Scholar
White, T.J., Bruns, T.D., Lee, S.B. & Taylor, J.W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR – Protocols and Applications – A Laboratory Manual, ed. Innis, N., Gelfand, D., Sninsky, J. & White, T., pp. 315–322. Academic Press, New York.Google Scholar
Willerslev, E. & Cooper, A. (2005). Ancient DNA. Proc. R. Soc. B 272, 3–16.CrossRefGoogle ScholarPubMed
Willerslev, E., Hansen, A.J., Binladen, J., Brand, T.B., Gilbert, M.T., Shapiro, B., Bunce, M., Wiuf, C., Gilichinsky, D.A. & Cooper, A. (2003). Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300, 791–795.CrossRefGoogle ScholarPubMed
Willerslev, E., Hansen, A.J., Ronn, R., Brand, T.B., Barnes, I., Wiuf, C., Gilichinsky, D.A. & Cooper, A. (2004). Long-term persistence of bacterial DNA. Curr. Biol. 14, R9–R10.CrossRefGoogle ScholarPubMed
Wilson, P.K. (2007). Development of life marker chip technology for in-situ life detection on Mars. PhD Thesis, Cranfield University, http://dspace.lib.cranfield.ac.uk/handle/1826/4617Google Scholar
Woese, C. (1987). Bacterial evolution. Microbiol. Rev. 51, 221–271.CrossRefGoogle ScholarPubMed