Hostname: page-component-cd9895bd7-gxg78 Total loading time: 0 Render date: 2024-12-28T03:07:29.116Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular characterization of ancient algal mats from the McMurdo Dry Valleys, Antarctica

Published online by Cambridge University Press:  15 November 2011

Doug E. Antibus ,
Laura G. Leff ,
Brenda L. Hall ,
Jenny L. Baeseman  and
Christopher B. Blackwood
Doug E. Antibus*
Affiliation:
Department of Biological Sciences, 256 Cunningham Hall, Kent State University, Kent, OH 44242, USA Room 3316, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, IL 61604, USA
Laura G. Leff
Affiliation:
Department of Biological Sciences, 256 Cunningham Hall, Kent State University, Kent, OH 44242, USA
Brenda L. Hall
Affiliation:
Department of Earth Sciences, 5790 Bryand Global Sciences Center, Orono, ME 04469-5790, USA
Jenny L. Baeseman
Affiliation:
International Arctic Research Center, University of Alaska Fairbanks, PO Box 757340, Fairbanks, AK 99775-7340, USA
Christopher B. Blackwood
Affiliation:
Department of Biological Sciences, 256 Cunningham Hall, Kent State University, Kent, OH 44242, USA
*
dantibus@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

The McMurdo Dry Valleys possess a cold and dry climate which favours biomolecular preservation, and present the possibility for preservation of biological materials over long timescales. We examined patterns of bacterial DNA abundance and diversity in algal mats from 8–26 539 years of age. Bacterial DNA abundance was inferred from extractable DNA quantity and quantitative polymerase chain reaction targeting the bacterial 16S rRNA gene. Because damage to bacterial DNA could limit its availability for polymerase chain reaction, the efficacy of DNA repair by a commercially available kit was also examined. Polymerase chain reaction amplicons of the bacterial 16S rRNA gene were obtained from seven of eight samples. Bulk DNA abundance and bacterial 16S rRNA gene copy number of template DNA declined with increasing sample age consistent with expectations of accumulation of DNA damage in ancient materials. Clone libraries revealed age related patterns of abundance for some bacterial phylogenetic groups. For example, Firmicutes and several other lineages were abundant in ancient samples, but Cyanobacteria were absent. This points to a biased persistence of bacterial lineages that change over time since photosynthesis was active.

Keywords

ancient bacterial DNAmicrobial dormancyVictoria Land16S rRNA
Type
Biological Sciences
Information
Antarctic Science , Volume 24 , Issue 2 , 28 February 2012 , pp. 139 - 146
Copyright
Copyright © Antarctic Science Ltd 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aislabie, J.M., Jordan, S.Barker, G.M. 2008. Relation between soil classification and bacterial diversity in soils of the Ross Sea region, Antarctica. Geoderma, 144, 9–20.CrossRefGoogle Scholar
Aislabie, J.M., Chhour, K., Saul, D.J., Miyauchi, S., Ayton, J., Paetzold, R.F.Balks, M.R. 2006. Dominant bacteria in soils of Marble Point and Wright Valley, Victoria Land, Antarctica. Soil Biology and Biochemistry, 38, 3041–3056.CrossRefGoogle Scholar
Barns, S.M., Fundyga, R.E., Jeffries, M.W.Pace, N.R. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proceedings of the National Academy of Sciences of the United States of America, 91, 1609–1613.CrossRefGoogle Scholar
Billi, D.Potts, M. 2002. Life and death of dried prokaryotes. Research in Microbiology, 153, 7–12.CrossRefGoogle ScholarPubMed
Blackwood, C.B., Oaks, A.Buyer, J.S. 2005. Phylum- and class-specific PCR primers for general microbial community analysis. Applied and Environmental Microbiology, 71, 6193–6198.CrossRefGoogle ScholarPubMed
Bowman, J.P., Rea, S.M., McCammon, S.A.McMeekin, T.A. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environmental Microbiology, 2, 227–237.CrossRefGoogle Scholar
Brambilla, E., Hippe, H., Hagelstein, A., Tindall, B.J.Stackebrandt, E. 2001. 16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antarctica. Extremophiles, 5, 23–33.CrossRefGoogle ScholarPubMed
Christner, B.C., Mosley-Thompson, E., Thompson, L.G.Reeve, J.N. 2003. Bacterial recovery from ancient glacial ice. Environmental Microbiology, 5, 433–436.CrossRefGoogle ScholarPubMed
Davey, M.C. 1989. The effects of freezing and desiccation on photosynthesis and survival of terrestrial Antarctic algae and cyanobacteria. Polar Biology, 10, 29–36.CrossRefGoogle Scholar
Doran, P.T., McKay, C.P., Clow, G.D., Dana, G.L., Fountain, A.G., Nylen, T.Lyons, W.B. 2002. Valley floor climate observations from the McMurdo Dry Valleys, Antarctica, 1986–2000. Journal of Geophysical Research, 107, 1–12.CrossRefGoogle Scholar
Ellis-Evans, J.C. 1996. Microbial diversity and function in Antarctic freshwater ecosystems. Biodiversity and Conservation, 11, 1395–1431.CrossRefGoogle Scholar
Feinstein, L.M., Sul, W.J.Blackwood, C.B. 2009. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Applied Environmental Microbiology, 75, 5428–5433.CrossRefGoogle ScholarPubMed
Fierer, N., Jackson, J.A., Vilgalys, R.Jackson, R.B. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied Environmental Microbiology, 71, 4117–4120.CrossRefGoogle ScholarPubMed
Friedmann, E.I., Kappen, L., Meyer, M.A.Nienow, J.A. 1993. Long-term productivity in the cryptoendolithic microbial community of the Ross Desert, Antarctica. Microbial Ecology, 25, 51–69.CrossRefGoogle ScholarPubMed
Gilichinsky, D.A., Wilson, G.S., Friedmann, E.I.et al. 2007. Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology. Astrobiology, 7, 275–311.CrossRefGoogle ScholarPubMed
Hall, B.L.Denton, G.H. 2000. Radiocarbon chronology of Ross Sea drift, eastern Taylor Valley, Antarctica: evidence for a grounded ice sheet in the Ross Sea at the Last Glacial Maximum. Geografiska Annaler, 82A, 305–336.CrossRefGoogle Scholar
Hall, B.L., Denton, G.H.Overturf, B. 2001. Glacial Lake Wright, a high-level Antarctic lake during the LGM and early Holocene. Antarctic Science, 13, 53–60.CrossRefGoogle Scholar
Hall, B.L., Denton, G.H., Overturf, B.Hendy, C.H. 2002. Glacial Lake Victoria, a high-level Antarctic lake inferred from lacustrine deposits in Victoria Valley. Journal of Quaternary Science, 17, 697–706.CrossRefGoogle Scholar
Hawes, I., Howard-Williams, C.Vincent, W.F. 1992. Dessication and recovery of Antarctic cyanobacterial mats. Polar Biology, 12, 587–594.CrossRefGoogle Scholar
Johnson, S.S., Hebsgaard, M.B., Christensen, T.R., Mastepanov, M., Nielsen, R., Munch, K., Brand, T., Gilbert, M.T.P., Zuber, M.T., Bunce, M., Rønn, R., Gilichinsky, D., Froese, D.Willerslev, E. 2007. Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences of the United States of America, 104, 14 401–14 405.CrossRefGoogle ScholarPubMed
Kennedy, M.J., Reader, S.L.Swierczynski, L.M. 1994. Preservation records of micro-organisms: evidence of the tenacity of life. Microbiology Reading English, 140, 2513–2529.CrossRefGoogle ScholarPubMed
Legendre, P.Anderson, M.J. 1999. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecological Monographs, 69, 1–24.CrossRefGoogle Scholar
Lozupone, C., Hamady, M.Knight, R. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics, 7, 371.CrossRefGoogle Scholar
McKnight, D., Tate, C., Andrews, E., Niyogi, D., Cozzetto, K., Welch, K., Lyons, W.Capone, D. 2007. Reactivation of a cryptobiotic stream ecosystem in the McMurdo Dry Valleys, Antarctica: a long-term geomorphological experiment. Geomorphology, 89, 186–204.CrossRefGoogle Scholar
Moodley, K. 2004. Microbial diversity of Antarctic dry valley mineral soil. MSc thesis, University of the Western Cape, 103 pp. [Unpublished.]Google Scholar
Moorhead, D.L., Doran, P.T., Fountain, A.G., Lyons, W.B., McKnight, D.M., Priscu, J.C., Virginia, R.A.Wall, D.H. 1999. Ecological legacies: impacts on ecosystems of the McMurdo Dry Valleys. BioScience, 49, 1009–1019.CrossRefGoogle Scholar
Paerl, H.W., Pinckney, J.L.Steppe, T.F. 2000. Cyanobacteria and bacterial mat consortia: examining the functional unit of microbial survival and growth in extreme environments. Environmental Microbiology, 2, 11–26.CrossRefGoogle ScholarPubMed
Ritchie, P.A., Millar, C.D., Gibb, G.C., Baroni, C.Lambert, D.M. 2004. Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adélie penguin lineages in Antarctica. Molecular Biology and Evolution, 21, 240–248.CrossRefGoogle ScholarPubMed
Rivkina, E.M., Friedmann, E.I., McKay, C.P.Gilichinsky, D.A. 2000. Metabolic activity of permafrost bacteria below the freezing Point. Applied and Environmental Microbiology, 66, 3230–3233.CrossRefGoogle ScholarPubMed
Rollo, F., Luciani, S., Marota, I., Olivieri, C.Ermini, L. 2007. Persistence and decay of the intestinal microbiota's DNA in glacier mummies from the Alps. Journal of Archaeological Science, 34, 1294–1305.CrossRefGoogle Scholar
Šabacká, M.Elster, J. 2006. Response of cyanobacteria and algae from Antarctic wetland habitats to freezing and desiccation stress. Polar Biology, 30, 31–37.CrossRefGoogle Scholar
Schloss, P.D.Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species-richness. Applied and Environmental Microbiology, 71, 1501–1506.CrossRefGoogle ScholarPubMed
Shirkey, B., McMaster, N.J., Smith, S.C., Wright, D.J., Rodriguez, H., Jaruga, P., Birincioglu, M., Helm, R.F.Potts, M. 2003. Genomic DNA of Nostoc commune (Cyanobacteria) becomes covalently modified during long-term (decades) desiccation but is protected from oxidative damage and degradation. Nucleic Acids Research, 31, 2995–3005.CrossRefGoogle ScholarPubMed
Smith, J.J., Tow, L.A., Stafford, W., Cary, C.Cowan, D.A. 2006. Bacterial diversity in three different Antarctic cold desert mineral soils. Microbial Ecology, 51, 413–421.CrossRefGoogle ScholarPubMed
Stackebrandt, E.Goebel, B.M. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology, 44, 846–849.Google Scholar
Suzina, N.E., Mulyukin, A.L., Kozlova, A.N., Shorokhova, A.P., Dmitriev, V.V., Barinova, E.S., Mokhova, O.N., El’-Registan, G.I.Duda, V.I. 2004. Ultrastructure of resting cells of some non-spore-forming bacteria. Microbiology, 73, 435–447.CrossRefGoogle ScholarPubMed
Van Trappen, S., Mergaert, J., van Eygen, S., Dawyndt, P., Cnockaert, M.C.Swings, J. 2002. Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes. Systematic and Applied Microbiology, 25, 603–610.CrossRefGoogle ScholarPubMed
Vincent, W.F. 2000. Evolutionary origins of Antarctic microbiota: invasion, selection and endemism. Antarctic Science, 12, 374–385.CrossRefGoogle Scholar
Wang, Q., Garrity, G.M., Tiedje, J.M.Cole, J.R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261–5267.CrossRefGoogle ScholarPubMed
Willerslev, E.Cooper, A. 2005. Ancient DNA. Proceedings of the Royal Society, B272, 3–16.Google Scholar