Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals

Canadian Journal of Microbiology

Volumn 51, Issue 11, 2005, Pages 910-923

  Radeva, Galina ^a,b   Selenska Pobell, Sonja ^a  

^a INSTITUTE OF ION BEAM PHYSICS AND MATERIALS RESEARCH   (Germany)

^b INSTITUTE OF MOLECULAR BIOLOGY   (Bulgaria)

Author keywords

16S rDNA; Bacterial diversity; Ribosomal intergenic spacer amplification (RISA); Uranium wastes

Indexed keywords

16S RDNA; BACTERIAL DIVERSITY; RIBOSOMAL INTERGENIC SPACER AMPLIFICATION (RISA); URANIUM WASTES;

BACTERIA; CLONING; DNA; RADIOACTIVE WASTES; URANIUM; URANIUM MINES;

BIODIVERSITY;

DNA 16S; SPACER DNA; URANIUM;

BACTERIUM; MINING; SPECIES DIVERSITY; URANIUM; WASTE;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; BACTEROIDES; CLONE; CYTOPHAGA; DELTAPROTEOBACTERIA; FLAVOBACTERIA; FRAUTERIA; GENE AMPLIFICATION; GENE SEQUENCE; GERMANY; MICROBIAL DIVERSITY; NITROSPINA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS; RADIOACTIVE WASTE; UNINDEXED SEQUENCE; UNITED STATES; WATER SAMPLING;

BACTERIA; BACTEROIDES; BIODIVERSITY; CYTOPHAGA; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA, RIBOSOMAL SPACER; FLAVOBACTERIUM; GERMANY; INDUSTRIAL WASTE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROTEOBACTERIA; PSEUDOMONAS; RADIOACTIVE POLLUTANTS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; UNITED STATES; URANIUM; WASTE DISPOSAL, FLUID; WATER MICROBIOLOGY;

CENTRAL EUROPE; EURASIA; EUROPE; GERMANY;

ACINETOBACTER; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDES; CYTOPHAGA; DELTAPROTEOBACTERIA; FLAVOBACTERIA; FLAVOBACTERIUM; NITROSOMONAS SP.; NITROSPINA; PROTEOBACTERIA; PSEUDOMONAS;

EID: 33144476849     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/w05-082     Document Type: Article

References (61)

1. Acinas, S.G., Anton, J., and Rodriguez-Valera, F. 1999. Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65: 514-522.
2. Alfreider, A., Vogt, C., and Babel, W. 2002. Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst. Appl. Microbiol. 25: 232-240.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
4. Borneman, J., and Triplett, E.W. 1997. Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and populations shifts associated with deforestation. Appl. Environ. Microbiol. 63: 2647-2653.
5. Bowman, J.P., and Nichols, D.S. 2002. Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats. Int. J. Syst. Evol. Microbiol. 52: 1533-1541.
6. Carroll, A.B., and Zinder, S.H. 2002. (Cornell University.) Unpublished data.
7. Chang, Y., Peacock, A.D., Long, P., Stephen, J., McKinley, J.P., Macnaughton, S.J., et al. 2001. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol. 67: 3149-3160.
8. Coates, J.D., Cole, K.A., Chakraborty, R., O'Connor, S.M., and Achenbach, L.A. 2002. Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration. Appl. Environ. Microbiol. 68: 2445-2452.
9. Derakshani, M., Lukow, T., and Liesack, W. 2001. Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67: 623-631.
10. Dojka, M.A., Harris, J.K., and Pace, N.R. 2000. Expanding the known diversity and environmental distribution of a uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66: 1617-1621.
11. Douglas, S., and Beveridge, T.J. 1998. Mineral formation by bacteria in natural microbial communities. FEMS Microbiol. Ecol. 26: 79-88.
12. Dunbar, J., Barns, S.M., Ticknor, L.O., and Kuske, C.R. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68: 3035-3044.
13. Egli, K., Fanger, U., Alvarez, P.J.J., Siegrist, H., Van der Meer, J.R., and Zehnder, A.J.B. 2001. Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate. Arch. Microbiol. 175: 198-207.
14. Felsenstein, J. 1993. PHYLIP - phytogeny inference package version 3.5c [computer program]. Department of Genetics, University of Washington, Seattle, Washington.
15. Fields, M.W., Carroll, S.L., Rhee, S.-K., Bergman, K., Yan, T., and Zhou, J. 2004. (Miami University.) Unpublished data.
16. Fisher, M.M., and Triplett, E.W. 1999. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65: 4630-4636.
17. Flemming, K., Satschanska, G., and Selenska-Pobell, S. 2000. Comparison of the structures of natural bacterial communities in a uranium mining waste pile and in uranium mill tailings. Rep. 318. Forschungszentrum Rossendorf, Dresden, Germany.
18. Francis, A.J. 1990. Microbial dissolution and stabilisation of toxic metals and radionuclides in mixed wastes. Experientia (Basel), 46: 840-851.
19. Francis, A.J., and Dodge, C.J. 1998. Remediation of soils and wastes contaminated with uranium and toxic metals. Environ. Sci. Technol. 32: 3993-3998.
20. Gatzweiler, R., Jakubick, A.T., Meyer, J., Paul, M., and Schreyer, J. 2002. Flooding of the WISMUT mines - learning by doing or applying a comprehensive systematic approach? In Uranium in the aquatic environment. Edited by B.J. Merkel, B. Planer-Friedrich, and C. Wolkersdorfer. Springer-Verlag, Berlin, Heidelberg, and New York. pp. 745-754.
21. Geibler, A. 2003. Molekulare analyse der bakteriellen diversität in uranabfallhalden. Diploma thesis, Forschungszentrum Rossendorf, Dresden, Germany.
22. Geibler, A., Tzvetkova, T., Flemming, K., and Selenska-Pobell, S. 2004. Bacterial diversity in soils of the uranium mining wastes. Rep. 400. Forschungszentrum Rossendorf, Dresden, Germany.
23. Helling, C. 1999. Hydrogeochemische Untersuchungen an müllüberlagerten urantailings unter dem aspekt einer effektiven langzeitüberwachung. Wiss. Mitt. 9: 35-75.
24. Holmes, A.J., Tujula, N.A., Holley, M., Contos, A., James, J.M., Rogers, P., and Gillings, M.R. 2001. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia. Environ. Microbiol. 3: 256-264.
25. Huber, T., Faulkner, G., and Hugenholtz, P. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (Oxf.), 20: 2317-2319.
26. Hugenholtz, P., Pitulle, C., Hershberger, K.L., and Pace, N.R. 1998. Novel division level bacterial diversity in a Yellowstone Hot Spring. J. Bacteriol. 180: 366-376.
27. Hugenholtz, P., Tyson, G.W., Webb, R.I., Wagner, A.M., and Blackall, L.L. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67: 411-419.
28. Ivanova, I., Stephen, J.R., Chang, Y.-J., Briiggemann, J., Long, P.E., McKinley, J.P., et al. 2000. A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the β-subdivision of the class Proteobacteria in contaminated groundwater. Can. J. Microbiol. 46: 1012-1020.
29. Johnson, B.D., Rolfe, S., Hallberg, K.B., and Iversen, E. 2001. Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ. Microbiol. 3: 630-637.
30. Lloyd, J.R., and Lovley, D.R. 2001. Microbial detoxification of metals and radionuclides. Curr. Opin. Biotechnol. 12: 248-253.
31. Lopez-Garcia, P., Lopez-Lopez, A., Moreira, D., and Rodrigues-Valera, F. 2001. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic polar front. FEMS Microbiol. Ecol. 36: 193-202.
32. Lovley, D.R., and Lloyd, J.R. 2000. Microbes with a mettle for bioremediation. Nat. Biotechnol. 18: 600-601.
33. Maidak, B.L., Cole, J.R., Parker, C.T., Garrity, G.M., Larsen, N., Li, B., et al. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171-173.
34. Martinez-Garcia, J., Acinas, S.G., Anton, A.I., and Rodrigez-Valera, F. 1999. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods, 36: 55-64.
35. Merroun, M., Raff, J., Rossberg, A., Hennig, C., and Selenska-Pobell, S. 2005. Complexation of uranium by cells and S-layer sheets of Bacillus sphaericus JG A12. Appl. Environ. Microbiol. 71: 5532-5543
36. Meusnier, I., Olsen, J.L., Stam, W.T., Destombe, C., and Valero, M. 2001. Phylogenetic analyses of Caulerpa taxifolia (Chlorophyta) and of its associated bacterial microflora provide clues to the origin of the Mediterranean introduction. Mol. Ecol. 10: 931-946.
37. Meyer, J., Jenk, U., Göhrs, A., and Schuppan, W. 2002. Characterization of final mine flooding at the Schlema/Alberoda site of WISMUT GmbH with particular emphasis on flooding ware quality evolution. In Uranium in the aquatic environment. Edited by B.J. Merkel, B. Planer-Friedrich, and C. Wolkersdorfer. Springer-Verlag, Berlin, Heidelberg, and New York. pp. 769-774.
38. Nakabachi, A., Ishikawa, H., and Kudo, T. 2003. Extraordinary proliferation of microorganisms in aposymbiotic pea aphids, Acyrthosiphon pisum. J. Invertebr. Pathol. 82: 152-161.
39. Nevin, K.P., Finneran, K.T., and Lovley, D. 2003. Microorganisms associated with uranium bioremediation in a high-salinity subsurface sediment. Appl. Environ Microbiol. 69: 3672-3675.
40. Poly, F., Gros, R., Jocteur-Monrozier, L., and Perrodin, Y. 2002. Short-term changes in bacterial community fingerprints and potential activities in an alfisol supplemented with solid waste leachates. Environ. Sci. Technol. 36: 4729-4734.
41. Purkhold, U., Timmermann, G., Koops, H.P., Pommerening-Roeser, A., and Wagner, M. 2002. (Technische Universitet Muenchen, Germany.) Unpublished data.
42. Raff, J., Soltmann, U., Matys, S., Schnorpfeil, M., Böttcher, H., Pompe, W., and Selenska-Pobell, S. 2002. Bacteria-based bioremediation of uranium mining waste waters by using sol-gel ceramics. In Uranium in the aquatic environment. Edited by B.J. Merkel, B. Planer-Friedrich, and C. Wolkersdorfer. Springer-Verlag, Berlin, Heidelberg, and New York. pp. 615-622.
43. Raff, J., Soltmann, U., Matys, S., Selenska-Pobell, S., Böttcher, H., and Pompe, W. 2003. Biosorption of uranium and copper by biocers. Chem. Mater. 15: 240-244.
44. Raff, J., Merroun, M., Rossberg, A., Soltmann, U., and Selenska-Pobell, S. 2004. Interactions of the U mining waste pile isolate Bacillus sphaericus JG-A12 with uranium. In Water rock interaction. Edited by R.B. Wanty and R.R. Seal. Balkema Publishers, Leiden, Netherlands. pp. 697-701.
45. Ravenschlag, K., Sahm, K., Knoblauch, C., Jorgersen, B.B., and Amann, R. 2000. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol. 66: 3592-3602.
46. Reysenbach, A.L., Longnecker, K., and Kirshtein, J. 2000. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a mid-atlantic ridge hydrothermal vent. Appl. Environ. Microbiol. 66: 3798-3806.
47. Satschanska, G., Golovinsky, E., and Selenska-Pobell, S. 2004. Bacterial diversity in a soil sample from a uranium mining waste pile as estimated via a culture-independent 16S rDNA approach. C.R. Acad. Bulg. Sci. 57: 75-82.
48. Schloss, P.D., and Handelsman, J. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68: 686-691.
49. Schloss, P.D., and Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501-1506.
50. Schmid, M., Twachtmann, U., Klein, M., Strous, M., Jetten, M., Metzger, J.W., et al. 2000. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst. Appl. Microbiol. 23: 93-106.
51. Schmid, M., Schmitz-Esser, S., Jetten, M., and Wagner, M. 2001. 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ. Microbiol. 3: 450-459.
52. Selenska-Pobell, S. 2002. Diversity and activity of bacteria in uranium waste piles. In Interactions of microorganisms with radionuclides. Edited by M. Keth-Roach and F. Livens. Elsevier Sciences, Oxford, U.K. pp. 225-253.
53. Selenska-Pobell, S., and Evguenieva-Hackenberg, E. 1995. Fragmentations of the large-subunit rRNA in the family Rhizobiaceae. J. Bacteriol. 177: 6993-6998.
54. Selenska-Pobell, S., Kampf, G., Flemming, K., Radeva, G., and Satchanska, G. 2001. Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval. Antonie Leeuwenhoek, 79: 149-161.
55. Selenska-Pobell, S., Flemming, K., Tzvetkova, T., Raff, J., Schnorpfeil, M., and Geibler, A. 2002. Bacterial communities in uranium mining waste piles and their interaction with heavy metals. In Uranium in the aquatic environment. Edited by B.J. Merkel, B. Planer-Friedrich, and C. Wolkersdorfer. Springer-Verlag, Berlin, Heidelberg, and New York. pp. 455-464.
56. Soltmann, U., Raff, J., Selenska-Pobell, S., Matys, S., Pompe, W., and Böttcher, H. 2003. Biosoption of heavy metals by sol-gel immobilized Bacillus sphaericus cells, spores and S-layers. J. Sol-Gel Sci. Technol. 26: 1209-1212.
57. Stein, L.Y., Jones, G., Alexander, B., Elmund, K., Wright-Jones, C., and Nealson, K.H. 2002. Intriguing microbial diversity associated with metal-rich particles from freshwater reservoir. FEMS Microbiol. Ecol. 42: 431-440.
58. Suzuki, Y., and Banfield, J.F. 1999. Geomicrobiology of uranium. In Uranium: mineralogy, geochemistry and the environment. Edited by P.C. Burns and R. Finch. Mineralogical Society of America, Washington, D.C. pp. 415-420.
59. Teske, A., Aim, E., Regan, J.M., Toze, S., Rittmann, B.E., and Stahl, D.A. 1994. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176: 6623-6630.
60. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
61. Van der Meer, J., Werlen, C., and Siegrist, H. 1998. (EAWAG Swiss Federal Institute for Environmental Science and Technology.) Unpublished data.