JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Genomic DNA Extracted from Ancient Antarctic Glacier Ice for Molecular Analyses on the Indigenous Microbial Communities
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
  • Journal title : Ocean and Polar Research
  • Volume 27, Issue 2,  2005, pp.205-214
  • Publisher : Korea Institute of Ocean Science & Technology
  • DOI : 10.4217/OPR.2005.27.2.205
 Title & Authors
Genomic DNA Extracted from Ancient Antarctic Glacier Ice for Molecular Analyses on the Indigenous Microbial Communities
Lee, Sang-Hoon; Bidle, Kay; Falkowski, Paul; Marchant, David;
  PDF(new window)
 Abstract
From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria , Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.
 Keywords
Microbial diversity;Antarctic bacteria;Glacial microbiology;Ancient genes;
 Language
English
 Cited by
1.
경기만 해역에서 분리된 Skeletonema marinoi-dohrnii complex의 생장률에 대한 수온과 광도의 영향,송태윤;유만호;이영주;최중기;

환경생물, 2014. vol.32. 2, pp.118-128 crossref(new window)
 References
1.
Brinkmeyer, R., K. Knittel, J. Jurgens, H. Weyland, R. Amann, and E. Helmke. 2003. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl. Environ. Microbiol., 69, 6610-6619. crossref(new window)

2.
Beja, O., L. Aravind, E.V. Koonin, M.T. Suzuki, A. Hadd, L.P. Nguyen, S.B. Jovanovich, C.M. Gates, R.A. Feldman, J.L. Spudich, E.L. Spudich, and E.F. DeLong. 2000. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science, 289, 1902-1906. crossref(new window)

3.
Beja, O., M.T. Suzuki, J.F. Heidelberg, W.C. Nelson, C.M. Preston, T. Hamada, J.A. Eisen, C.M. Fraser, and E.F. DeLong. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature, 415, 630-633. crossref(new window)

4.
Carpenter, E.J., S. Lin, and D.G. Capone. 2000. Bacterial activity in South Pole snow. Appl. Environ. Microbiol., 66, 4514-4517. crossref(new window)

5.
Christner, B.C., E. Mosley-Thompson, L.G. Thompson, and J.N. Reeve. 2003. Bacterial recovery from ancient glacier ice. Environ. Microbiol., 5, 433-436. crossref(new window)

6.
Christner, B.C., E. Mosley-Thompson, L.G. Thompson, and J.N. Reeve. 2001. Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ. Microbiol., 3, 570-577. crossref(new window)

7.
DeLong, E.F. 1992. Archaea in coastal marine environments. Proc. Nat. Acad. Sci. USA., 89, 5685-5689. crossref(new window)

8.
Karl, D.M., D.F. Bird, K. Bjorkman, T. Houlihan, R. Shackelford, and L. Tupas. 1999. Microorganisms in the accreted ice of Lake Vostok, Antarctica. Science, 286, 2144-2147. crossref(new window)

9.
Lane, D.J. 1991. 16S/23S rRNA sequencing. p. 115-175. In: Nucleic acid techniques in bacterial systematics. eds by E. Stackebrandt and M. Goodfellow. Wiley, New York.

10.
Lee, S. and J. Fuhrman. 1991. Species composition shift of confined bacterioplankton studied at the level of community DNA. Mar. Ecol. Prog. Ser., 79, 195-201. crossref(new window)

11.
Ludwig, W., S.H. Bauer, M. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K.H. Schleifer. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett., 153, 181-190. crossref(new window)

12.
Marchant, D.R., A.R. Lewis, W.M. Phillips, E.J. Moore, R.A. Souchez, G.H. Denton, D.E. Sugden, N. Potter, Jr., and G.P. Landis. 2002. Formation of patterned ground and sublimation till over Miocene glacier ice in Beacon Valley, southern Victoria Land, Antarctica. Geol. Soc. Am. Bull., 114, 718-730. crossref(new window)

13.
Miteva, V.I., P.P. Sheridan, and J.E. Brenchley. 2004. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl. Environ. Microbiol., 70, 202-213. crossref(new window)

14.
Noble, R.T. and J.A. Fuhrman. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol., 14, 113-118. crossref(new window)

15.
Pace, N.R., D.A. Stahl, D.J. Lane, and G.J. Olsen. 1986. The analysis natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol., 9, 1-55. crossref(new window)

16.
Pearce, D.A. 2003. Bacterioplankton community structure in a maritime Antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). Microb. Ecol., 46, 92-105. crossref(new window)

17.
Priscu, J.C., E.E. Adams, W.B. Lyons, M.A. Voytek, D.W. Mogk, R.L. Brown, C.P. McKay, C.D. Takacs, K.A. Welch, C.F. Wolf, J.D. Kirshtein, and R. Avci. 1999. Geomicrobiology of subglacial ice above Lake Vostok, Antarctica. Science, 286, 2141-2144. crossref(new window)

18.
Priscu, J.C., C.H. Fritsen, E.E. Adams, S.J. Giovannoni, H.W. Pearl, C.P. McKay, P.T. Doran, D.A. Gordon, B.D. Lanoil, and J.L. Pinckney. 1998. Perennial Antarctic lake ice: an oasis for life in a polar desert. Science, 280, 2095-2098. crossref(new window)

19.
Porter, K.G. and Y.S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr., 25, 943-948. crossref(new window)

20.
Sawstrom, C., P. Mumford, W. Marshall, A. Hodson, and J . Laybourn-Parry. 2002. The microbial communities and primary productivity of cryoconite holes in an Arctic glacier (Svalbard $79{^{\circ}C}$). Polar Biol., 25, 591-596.

21.
Schmidt, T.M., E.F. DeLong, and N.R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol., 173, 4371-4378.

22.
Shizuya, H., B. Birren, U.J. Kim, V. Mancino, T. Slepak, Y. Tachiiri, and M. Simon. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Nat. Acad. Sci. USA., 89, 8794-8797. crossref(new window)

23.
Sugden, D.E., D.R. Marchant, N. Potter, Jr., R.A. Souchez, G.H. Denton, C.C. Swisher III, and J.-L. Tison. 1995. Preservation of Miocene glacier ice in east Antarctica. Nature, 376, 412-414. crossref(new window)

24.
Suzuki, M.T. and S.J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixture of 16S rRNA genes by PCR. Appl. Environ. Microbiol., 62, 625-630.

25.
Tanner, M.A., B.M. Goebel, M.A. Dojka, and N.R. Pace. 1998. Specific ribosomal DNA sequences from diverse environmental settings correlated with experimental contaminants. Appl. Environ. Microbiol., 64, 3110-3113.

26.
Ward, D.M., R. Weller, and M.M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature, 345, 63-65. crossref(new window)