Microbial investigations in Opalinus Clay, an argillaceous formation under evaluation as a potential host rock for a radioactive waste repository

Geomicrobiology Journal

Volumn 25, Issue 5, 2008, Pages 240-249

  Poulain, Sebastien ^a   Sergeant, Claire ^a   Simonoff, Monique ^a   Le Marrec, Claire ^b   Altmann, Scott ^c  

^a CENTRE D ETUDES NUCLÉAIRES DE BORDEAUX GRADIGNAN   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c ANDRA   (France)

Author keywords

16S rRNA PCR; Autochthonous microorganisms; DNA sequencing; Opalinus clay

Indexed keywords

ARGILLACEOUS DEPOSIT; DNA; HOST ROCK; MICROBIAL ACTIVITY; MICROORGANISM; RADIOACTIVE WASTE; RADIONUCLIDE; REPOSITORY; RNA; SEDIMENTATION; TAXONOMY;

ALICYCLOBACILLUS; BACTERIA (MICROORGANISMS); SPHINGOMONAS;

EID: 46249122871     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450802153314     Document Type: Article

References (36)

1. Bakermans, C., Tsapin, A. I., Souza-Egipsy, V., Gilichinsky, D. A. and Nealson, K. H. (2003) Reproduction and metabolism at - 10°C of bacteria isolated from Siberian permafrost. Environ Microbiol, 5, pp. 321-326.
2. Bargagli, R., Stotnicki, M. L., Marri, L., Pepi, M., MacKenzie, A. and Agnorelli, C. (2004) New record of moss and thermophilic bacteria species and physico-chemical properties of geothermal soils on the northwest slope of Mt. Melbourne (Antarctica). Polar Biol, 27, pp. 423-431.
3. Boivin-Jahns, V., Ruimy, R., Bianchi, A., Daumas, S. and Christen, R. (1996) Bacterial diversity in a deep-subsurface clay environment. Appl Environ Microbiol, 62, pp. 3405-3412.
4. Cano, R. J. and Borucki, M. K. (1995) Revival and identification of bacterial spores in 25 to 40 million year old Dominican amber. Science, 268, pp. 1060-1064.
5. Chernyh, N. A., Gavrilov, S. N., Sorokin, V. V., German, K. E., Sergeant, C., Simonoff, M., Robb, F. and Slobodkin, A. I. (2007) Characterization of Technetium(VII) Reduction by cell suspensions of thermophilic bacteria and archae. Appl Microbiol Biotech, 76, pp. 467-472.
6. Christner, B. C., Mosley-Thompson, E., Thompson, L. G. and Reeve, J. N. (2001) Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ Microbiol, 3, pp. 5770-5777.
7. Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam, S. A., McGarrell, D. M., Garrity, G. M. and Tiedje, J. M. (2005) The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res, 33, pp. 294-296.
8. Connon, S. A., Tovanabootr, A., Dolan, M., Vergin, K., Giovannoni, S. J. and Semprini, L. (2005) Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environ Microbiol, 7, pp. 165-178.
9. Dong, W., Xie, G., Miller, T. R., Franklin, M. P., Oxenberg, T. P., Bouwer, E. J., Ball, W. P. and Halden, R. U. (2006) Sorption and bioreduction of hexavalent uranium at a military facility by the Chesapeake Bay. Environ Pollut, 142, pp. 132-142.
10. Fredrickson, J. K., Zachara, Z. M., Balkwill, D. L., Kennedy, D., Li, S. W., Kostandarithes, H. M., Daly, M. J., Romine, M. F. and Brockman, F. J. (2004) Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at Hanford site, Washington state. Appl Environ Microbiol, 70, pp. 4230-4241.
11. Fong, N JC, Burgess, N. L., Barrow, K. D. and Glenn, R. D. (2001) Carotenoid accumulation in the psychrotrophic bacterium Arthrobacter agilis in response to thermal and salt stress. Appl Microbiol Biotechnol, 56, pp. 750-756.
12. Jackson, C. R., Harper, J. P., Willoughby, D., Roden, E. E. and Churchill, P. F. (1997) A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl Environ Microbiol, 63, pp. 4993-4995.
13. Imperio, T., Viti, C. and Marri, L. (2008) Alicyclobacillus pohliae sp. nov., a thermophilic, endospore-forming bacterium isolated from geothermal soil of the north-west slope of Mount Melbourne (Antarctica). Int J Syst Evol Microbiol, 58, pp. 221-225.
14. Kumar, S., Tamura, K. and Nei, M. (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform, 5, pp. 150-163.
15. Lovley, D. R., Coates, J. D., Blunt-Harris, E. L., Phillips, E JP and Woodward, J. C. (1996) Humic substances as electron acceptors for microbial respiration. Nature, 382, pp. 445-448.
16. Martin-Laurent, F., Philippot, L., Hallet, S., Chaussod, R., Germon, J. C., Soulas, G. and Catroux, G. (2001) DNA extraction from soils: Old bias for new microbial diversity analysis methods. Appl Environ Microbiol, 67, pp. 2354-2359.
17. Mauclaire, L., McKenzie, J., Schwyn, B. and Bossart, P. (2007) Detection and identification of indigenous microorganisms in Mesozoic claystone core samples from the Opalinus Clay formation (Mont Terri Rock Laboratory). Phys Chem Earth, 32, pp. 232-240.
18. Miller, D. N., Bryant, J. E., Madsen, E. L. and Ghiorse, W. C. (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol, 65, pp. 4715-4724.
19. Miteva, V. I. and Brenchley, J. E. (2005) Detection and isolation of ultrasmall microorganisms from a 120,000-year-old Greenland glacier ice core. Appl Environ Microbiol, 71, pp. 7806-7818.
20. Miyoshi, T., Iwatsuki, T. and Naganuma, T. (2005) Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2 micrometer-pore-size-filters. Appl Environ Microbiol, 71, pp. 1084-1088.
21. Muyzer, G., Hottentrager, S., Teske, A. and Wawer, C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA-A new molecular approach to analyse the genetic diversity of mixed microbial communities. Molecular Microbial Ecology, Manual 3.4.4, pp. 1-23. Kluwer Academic Publishers, Dordrecht, The Netherlands
22. Onstott, T. C., Phelps, T. J., Colwell, F. S., Ringelberg, D., White, D. C., Boone, D. R., McKinley, J. P., Stevens, T. O., Long, P. E., Balkwill, D. L., Griffin, W. T. and Kieft, T. (1998) Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia. Geomicrobiol J, 15, pp. 353-385.
23. Pearson, F. J., Arcos, D., Bath, A., Boisson, J-Y, Fernandez, A. M., Gabler, H-E, Gaucher, E., Gautschi, A., Griffault, L., Hernan, P. and Waber, H. N. (2003) Mont Terri Project-Geochemistry of water in the Opalinus Clay formation at the Mont Terri rock laboratory. Reports of the FOWG, Geology Series-No. 5.
24. Pottu-Boumendil, J. (1989) Techniques en microscopie electronique - Principes et methodes de preparation.
25. Ruggiero, C. E., Boukhalfa, H., Forsythe, J. H., Lack, J. G., Hersman, L. E. and Neu, M. P. (2005) Actinide and metal toxicity to prospective bioremediation bacteria. Environ Microbiol, 7, pp. 88-97.
26. Sammartino, S., Bouchet, A., Pret, D., Parneix, J-C and Tevissen, E. (2003) Spatial distribution of porosity and minerals in clay rocks from the Callovo-Oxfordian formation (Meuse/Haute-Marne, Eastern France)-implications on ionic species diffusion and rock sorption capability. Appl Clay Sci, 23, pp. 157-166.
27. Scala, D. J., Hacherl, E. L., Cowan, R., Young, L. Y. and Kosson, D. S. (2006) Characterization of Fe(III)-reducing enrichment cultures and isolation of Fe(III)-reducing bacteria from the Savannah River site, South Carolina. Res Microbiol, 157, pp. 772-783.
28. Simonoff, M., Sergeant, C., Poulain, S. and Pravikoff, M. S. (2007) Microorganisms and migration of radionuclides in environment. CR Chimie, 10, pp. 1092-1107.
29. Soina, V. S., Mulyukin, A. L., Demkina, E. V., Vorobyova, E. A. and El-Registan, G. I. (2004) The structure of resting bacterial populations in soil and subsoil permafrost. Astrobiology, 4, pp. 345-358.
30. Stroes-Gascoyne, S., Schippers, A., Schwyn, B., Poulain, S., Sergeant, C., Le Marrec, C, Simonoff, M., Altmann, S., Nagaoka, T., Mauclaire, L., McKenzie, J., Daumas, S., Vinsot, A., Beaucaire, C. and Matray, J-M (2007) Microbial community analysis of Opalinus Clay drill core samples from the Mont Terri Underground Research Laboratory, Switzerland. Geomicrobiol J, 24, pp. 1-17.
31. Thury, M. (2002) The characteristics of the Opalinus Clay investigated in the Mont Terri underground rock laboratory in Switzerland. CR Physique, 3, pp. 923-933.
32. Vreeland, R. H., Rosenzweig, W. D. and Powers, D. W. (2000) Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature, 407, pp. 897-900.
33. Weisburg, W. G., Barns, S. M., Pelletier, D. A. and Lane, D. J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol, 173, pp. 697-703.
34. White, T. J., Bruns, T., Lee, S. and Taylor, J. W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, pp. 315-322. Academic Press, New York
35. Willerslev, E., Hansen, A. J., Rønn, R., Brand, T. B., Barnes, I., Wiuf, C., Gilichinsky, D., Mitchell, D. and Cooper, A. (2004) Long-term persistence of bacterial DNA. Curr Biol, 14, pp. 431-433.
36. Zhou, J., Bruns, M. A. and Tiedje, J. M. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol, 62, pp. 316-322.