Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site▽

Applied and Environmental Microbiology

Volumn 76, Issue 10, 2010, Pages 3106-3115

  Field, Erin K ^a   D'Imperio, Seth ^b   Miller, Amber R ^c   Vanengelen, Michael R ^b   Gerlach, Robin ^b   Lee, Brady D ^c   Apel, William A ^c   Peyton, Brent M ^b  

^a MONTANA STATE UNIVERSITY   (United States)

^b Montana State University   (United States)

^c IDAHO NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ACTINOBACTERIA; BACTERIAL COMMUNITY STRUCTURE; CARDBOARD BOXES; CELLULOSIC MATERIAL; CELLULOSIC WASTES; CLONE LIBRARY; COORDINATE ANALYSIS; DIVERSITY INDEX; IDAHO NATIONAL LABORATORIES; INTERFACE LAYER; MOLECULAR TECHNIQUES; NONRADIOACTIVE; SOIL MICROBIAL COMMUNITY; SOIL SAMPLE; STRATIFIED SOIL; U.S. DEPARTMENT OF ENERGY; WASTE SITES;

BACTERIA; BACTERIOLOGY; CHROMIUM; CLONING; GEOLOGIC MODELS; HEAVY METALS; LIBRARIES; RADIOACTIVE WASTES; RADIOACTIVITY; RNA; SOCIAL SCIENCES; SOILS; TRANSURANIUM ELEMENTS; URANIUM;

ENERGY CONVERSION;

CELLULOSE; RNA 16S; URANIUM;

BACTERIUM; BIODEGRADATION; CELLULOSE; COMMUNITY DYNAMICS; DIVERSITY INDEX; GENETIC ANALYSIS; HEAVY METAL; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; RADIOACTIVE WASTE; RADIONUCLIDE; SOIL MICROORGANISM; SPECIES DIVERSITY; URANIUM;

ACTINOBACTERIA; ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; BACTEROIDETES; BIODIVERSITY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POLLUTION; RADIOACTIVE WASTE; SOIL; SOIL POLLUTANT; UNITED STATES;

ACTINOBACTERIA; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BACTEROIDETES; BIODIVERSITY; CELLULOSE; IDAHO; MOLECULAR SEQUENCE DATA; RADIOACTIVE WASTE; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY; SOIL POLLUTANTS; URANIUM; WASTE PRODUCTS;

IDAHO; IDAHO NATIONAL LABORATORY; UNITED STATES;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES;

EID: 77952251339     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01688-09     Document Type: Article

References (61)

1. Abdelouas, A., W. Lutze, W. L. Gong, E. H. Nuttall, B. A. Strietelmeier, and B. J. Travis. 2000. Biological reduction of uranium in groundwater and subsurface soil. Sci. Total Environ. 250:21-35.
2. Anonymous. 1994. Radioactive waste disposal: an environmental perspective. Environmental Protection Agency, Washington, DC.
3. Anonymous. 2000. The current and planned low-level waste disposal capacity report, revision 2. Department of Energy, Washington, DC.
4. Bayer, E., Y. Shoham, and R. Lamed. 2006. Cellulose-decomposing bacteria and their enzyme systems, p. 578-617. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.2. Springer Science & Business Media, LLC, New York, NY.
5. Bentley, S., C. Corton, S. Brown, A. Barron, L. Clark, J. Doggett, B. Harris, D. Ormond, M. Quail, and G. May. 2008. Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J. Bacteriol. 190:2150-2160.
6. Brodie, E., T. Desantis, D. Joyner, S. Baek, J. Larsen, G. Andersen, T. Hazen, P. Richardson, D. Herman, T. Tokunaga, J. Wan, and M. Firestone. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 72:6288-6298.
7. Chew, I., J. Obbard, and R. Stanforth. 2001. Microbial cellulose decomposition in soils from a rifle range contaminated with heavy metals. Environ. Pollut. 111:367-375.
8. Choy, C., G. Korflatis, and X. Meng. 2006. Removal of depleted uranium from contaminated soils. J. Hazard. Mater. 136:53-60.
9. Coughlan, M., and F. Mayer. 1992. The cellulose-decomposing bacteria and their enzyme systems, p. 460-516. In A. Balows, H. G. Truper, M. Dworkin, W. Harder, and K. Schleifer (ed.), The prokaryotes, 2nd ed. vol 1. Springer Verlag, New York, NY.
10. DeSantis, T., Jr., P. Hugenholtz, K. Keller, E. Brodie, N. Larsen, Y. Piceno, R. Phan, and G. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:394-399.
11. DeSantis, T., E. Brodie, J. Moberg, I. Zubieta, Y. Piceno, and G. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371-383.
12. DeSantis, T., P. Hugenholtz, N. Larsen, M. Rojas, E. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. Andersen. 2006. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
13. Desvaux, M. 2005. Clostridium cellulolyticum: model organism of mesophilic cellulolytic Clostridia. FEMS Microbiol. Rev. 29:741-764.
14. Elshahed, M., N. Youssef, A. Spain, C. Sheik, F. Najar, L. Sukharnikov, B. Roe, J. Davis, P. Schloss, V. Bailey, and L. Krumholz. 2008. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl. Environ. Microbiol. 74:5422-5428.
15. Evtushenko, L., and M. Takeuchi. 2006. The family Microbacteriaceae, p. 1020-1098. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.3. Springer Science & Business Media, LLC, New York, NY.
16. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
17. Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Fhred. I. Accuracy assessment. Genome Res. 8:175-185.
18. Flanagan, J., E. Brodie, L. Weng, S. Lynch, O. Garcia, R. Brown, P. Hugenholtz, T. DeSantis, G. Andersen, J. Wiener-Kronish, and J. Bristow. 2007. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45:1954-1962. (Pubitemid 46933932)
19. Fox, J., R. Mortimer, G. Lear, J. Lloyd, I. Beadle, and K. Morris. 2006. The biogeochemical behaviour of U (VI) in the simulated near-field of a lowlevel radioactive waste repository. Appl. Geochem. 21:1539-1550.
20. Francis, A., S. Dobbs, and B. Nine. 1980. Microbial activity of trench leachates from shallow-land, low-level radioactive waste disposal sites. Appl. Environ. Microbiol. 40:108-113.
21. Francis, C., M. Timpson, and J. Wilson. 1999. Bench- and pilot-scale studies relating to the removal of uranium from uranium-contaminated soils using carbonate and citrate lixiviants. J. Hazard. Mater. 66:67-87.
22. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202. (Pubitemid 28177231)
23. Holmes, B. 2006. The genera Flavobacterium, Sphingobacterium, and eeksella, p. 539-548. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.7. Springer Science & Business Media, LLC, New York, NY.
24. Hreggvidsson, G., E. Kaiste, O. Hoist, G. Eggertsson, A. Palsdottir, and J. Kristjansson. 1996. An extremely thermostable cellulase from the thermophilic eubacterium Rhodothermus marinus. Appl. Environ. Microbiol. 62: 3047-3049.
25. Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319. (Pubitemid 39341624)
26. Hull, L., C. Grossman, R. Fjeld, J. Coates, and A. Elzerman. 2002. Estimating uranium partition coefficients from laboratory adsorption isotherms. INEEL/CON-02-00106. Idaho National Engineering and Environmental Laboratory, Idaho Falls, ID.
27. Humphreys, P., R. McGarry, A. Hoffmann, and P. Binks. 1997. DRINK: a biogeochemical source term model for low level radioactive waste disposal sites. FEMS Microbiol. Rev. 20:557-571.
28. Janssen, P. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719-1728.
29. Johansen, J., P. Nielsen, and C. Sjoholm. 1999. Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of Cytophaga fytica to Cellulophaga lytica gen. nov., comb, nov. Int. J. Syst. Evol. Microbiol. 49:1231-1240.
30. Kämpfer, P. 2006. The family Streptomycetaceae, part I: taxonomy, p. 538604. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.3. Springer Science & Business Media, LLC, New York, NY.
31. Kashefi, K., and D. Lovley. 2000. Reduction of Fe (III), Mn (IV), and toxic metals at 100°C by Pyrobaculum islandicum. Appl. Environ. Microbiol. 66: 1050-1056.
32. Keck, K., and R. Seitz. 2002. Potential for subsidence at the low-level radioactive waste disposal area. INEEL/EXT-02-01154. Idaho National Engineering and Environmental Laboratory, Idaho Falls, ID.
33. Khan, S., Y. Fukunaga, Y. Nakagawa, and S. Harayama. 2007. Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int. J. Syst. Evol. Microbiol. 57:2946-2951.
34. Khan, S., Y. Nakagawa, and S. Harayama. 2007. Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 57:265-269. (Pubitemid 46306450)
35. Kroppenstedt, R., and M. Goodfellow. 2006. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora, p. 682-724. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.3. Springer Science & Business Media, LLC, New York, NY.
36. Labeda, D., and R. Kroppenstedt. 2004. Emended description of the genus Glycomyces and description of Gfycomyces algeriensis sp. nov., Gfycomyces arizonensis sp. nov. and Gfycomyces lechevalierae sp. nov. Int. J. Syst. Evol. Microbiol. 54:2343-2346.
37. Labeda, D., R. Testa, M. Lechevalier, and H. Lechevalier. 1985. Gfycomyces, a new genus of theActinomycetales. Int. J. Syst. Evol. Microbiol. 35:417-421.
38. Leschine, S. 1995. Cellulose degradation in anaerobic environments. Annu. Rev. Microbiol. 49:399-426.
39. Liu, C., Y. Gorby, J. Zachara, J. Fredrickson, and C. Brown. 2002. Reduction kinetics of Fe (III), Co (III), U (VI), Cr (VI), and Tc (VII) in cultures of dissimilatory metal-reducing bacteria. Biotechnol. Bioeng. 80:637-649.
40. Lloyd, J., C. Harding, and L. Macaskie. 1997. Tc (VII) reduction and accumulation by immobilized cells of Escherichia coli. Biotechnol. Bioeng. 55:505-510.
41. Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
42. Ludwig, W., O. Strunk, R. Westram, L. Richter, and H. Meier. 2004. ARB: a Software environment for sequence data. Nucleic Acids Res. 32:1363-1371. (Pubitemid 38854737)
43. Lynd, L., P. Weimer, W. van Zyl, and I. Pretorius. 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66: 406-577.
44. 44. Means, J., D. Crerar, and J. Duguid. 1978. Migration of radioactive wastes: radionuclide mobilization by complexing agents. Science 200:1477-1481. (Pubitemid 8386755)
45. Ortiz-Bernad, I., R. Anderson, H. Vrionis, and D. Lovley. 2004. Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater. Appl. Environ. Microbiol. 70:3091-3095.
46. Peplies, J., R. Kottmann, W. Ludwig, and F. Glockner. 2008. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. J. Syst. Appl. Microbiol. 31:251-257.
47. Read, D., D. Ross, and R. Sims. 1998. The migration of uranium through Clashach Sandstone: the role of low molecular weight organics in enhancing radionuclide transport. J. Contam. Hydrol. 35:235-248.
48. Roh, Y., S. Liu, G. Li, H. Huang, T. Phelps, and J. Zhou. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl. Environ. Microbiol. 68:6013-6020.
49. Saeed, A., V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Klapa, T. Currier, and M. Thiagarajan. 2003. TM4: a free, opensource system for microarray data management and analysis. Biotechniques 34:45-51.
50. Safo-Sampah, S., and J. Torrey. 1988. Polysaccharide-hydrolyzing enzymes of Frankia (Actinomycetales). Plant Soil 112:89-97.
51. Sagaram, U., K. Deangelis, P. Trivedi, G. Andersen, S. Lu, and N. Wang. 2009. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus using PhyloChips and 16S rDNA clone library sequencing. Appl. Environ. Microbiol. 75:1566-1574.
52. Sani, R., B. Peyton, W. Smith, W. Apel, and J. Petersen. 2002. Dissimilatory reduction of Cr (VI), Fe (III), and U (VI) by Cellulomonas isolates. Appl. Microbiol. Biotechnol. 60:192-199.
53. Saunders, J., and L. Toran. 1995. Modeling of radionuclide and heavy metal sorption around low-arid high-pH waste disposal sites at Oak Ridge, Tennessee. Appl. Geochem. 10:673-684.
54. Schloss, P., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomie units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
55. Schloss, P., and J. Handelsman. 2006. Toward a census of bacteria in soil. PLoS Comput. Biol. 2:786-793.
56. Shelobolina, E., S. Sullivan, K O'Neill, K. Nevin, and D. Lovley. 2004. Isolation, characterization, and U (VI)-reducing potential of a facultatively anaerobic, acid-resistant bacterium from low-pH, nitrate-and U (VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov. Appl. Environ. Microbiol. 70:2959-2965.
57. Sunagawa, S., T. Desantis, Y. Piceno, E. Brodie, M. Desalvo, C. Voolstra, E. Weil, G. Andersen, and M. Medina. 2009. Bacterial diversity and white plague disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J. 3:512-521.
58. Thompson, E. 2002. Historical description of radioactive waste management complex (RWMC) surrogated buried waste test pits for environmental restoration (ER) waste area group 7 (WAG-7) operable unit (OU) 7-13 & 7-14. Idaho National Laboratory, Idaho Falls, ID.
59. Viamajala, S., B. Peyton, W. Apel, and J. Petersen. 2002. Chromate reduction in Shewanella oneidensis MR-1 is an inducible process associated with anaerobic growth. Biotechnol. Prog. 18:290-295.
60. Vilks, P., F. Caron, and M. Haas. 1998. Potential for the formation and migration of colloidal material from a near-surface waste disposal site. Appl. Geochem. 13:31-42.
61. Vobis, G. 2006. The genus Actinoplanes and related genera, p. 623-653. In M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 3rd ed., vol.3. Springer Science & Business Media, LLC, New York, NY.