Use of 16s rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment

FEMS Microbiology Reviews

Volumn 20, Issue 3-4, 1997, Pages 217-230

  Chandler, Darrell P ^a   Brockman, Fred J ^a   Fredrickson, Jim K ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

16S rRNA; Clone library; Polymerase chain reaction; Sediment; Subsurface

Indexed keywords

BACTERIAL GENE; BIOMASS; CONFERENCE PAPER; DNA SEQUENCE; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEDIMENT; SOIL MICROFLORA;

BACTERIA (MICROORGANISMS);

EID: 0030802010     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6445(97)00009-0     Document Type: Conference Paper

References (46)

1. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685-5689.
2. Barns, S.M., Fundyga, R.E., Jeffries, M.W. and Pace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91, 1609-1613.
3. Schmidt, T.M., DeLong, E.F. and Pace, N.R. (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173, 4371-4378.
4. Giovannoni, S.J., Britschgi, T.B., Moyer, C.L. and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63.
5. Liesack, W. and Stackebrandt, E. (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174, 5072-5078.
6. Pace, N.R., Stahl, D.A., Lane, D.J. and Olsen, G.J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9, 1-55.
7. Moyer, C.L., Dobbs, F.C. and Karl, D.M. (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60, 871-879.
8. McInerney, J.O., Wilkinson, M., Patching, J.W., Embley, T.M. and Powell, R. (1995) Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl. Environ. Microbiol. 61, 1646-1648.
9. Fuhrman, J.A., McCallum, K. and Davis, A.A. (1992) Novel major archaebacterial group from marine plankton. Nature 356, 148-149.
10. Ward, D.M., Weller, R.W. and Bateson, M.M. (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63-65.
11. Balkwill, D.L. (1989) Numbers, diversity, and morphological characteristics of aerobic, chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina. Geomicrobiol. J. 7, 33-52.
12. Fredrickson, J.K. et al. (1993) Microbiological characteristics of pristine and contaminated deep vadose sediments from an arid region. Geomicrobiol. J. 11, 95-107.
13. Fredrickson, J.K., Garland, T.R., Hicks, R.J., Thomas, J.M., Li, S.W. and McFadden, K.M. (1989) Lithotrophic and heterotrophic bacteria in deep subsurface sediments and their relation to sediment properties. Geomicrobiol. J. 7, 53-66.
14. Hicks, R.J. and Fredrickson, J.K. (1989) Aerobic metabolic potential of microbial populations indigenous to deep subsurface environments. Geomicrobiol. J. 7, 67-78.
15. Fredrickson, J.K., Balkwill, D.L., Drake, G.R., Romine, M.F., Ringelberg, D.B. and White, D.C. (1995) Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl. Environ. Microbiol. 61, 1917-1922.
16. Fredrickson, J.K., Balkwill, D.L., Zachara, J.M., Li, S.W., Brockman, F.J. and Simmons, M.A. (1991) Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the Atlantic coastal plain. Appl. Environ. Microbiol. 57, 402-411.
17. Brockman, F.J., Kieft, T.L., Fredrickson, J.K., Bjornstad, B.N., Li, S.W., Spangenburg, W. and Long, P.E. (1992) Microbiology of vadose zone paleosols in south-central Washington state. Microb. Ecol. 23, 279-301.
18. Stevens, T.O., McKinley, J.P. and Fredrickson, J.K. (1993) Bacteria associated with deep, alkaline, anaerobic groundwaters in southeast Washington. Microb. Ecol. 25, 35-50.
19. Brockman, F.J., Ringelberg, D.B., White, D.C., Fredrickson, J.K., Balkwill, D.L., Kieft, T.L., Phelps, T.J. and Ghiorse, W.C. (1993) Estimates of intact but nonviable and viable but nonculturable microorganisms in subsurface sediments from six boreholes located in wet and dry climatic regions of the United States. 1993 International Symposium on Subsurface Microbiology, B-32.
20. Kieft, T.L., Fredrickson, J.K., McKinley, J.P., Bjornstad, B.N., Rawson, S.A., Phelps, T.J., Brockman, F.J. and Pfiffner, S.M. (1995) Microbiological comparisons within and across contiguous lacustrine, paleosol, and fluvial subsurface sediments. Appl. Environ. Microbiol. 61, 749-757.
21. Hazen, T.C., Jimeniz, L., Lopez de Victoria, G. and Fliermans, C.B. (1991) Comparison of bacteria from deep subsurface sediment and adjacent groundwater. Microb. Ecol. 22, 293-304.
22. Brockman, F.J., Fredrickson, J.K., Li, S.W., Sun, W. and Kieft, T.L. (1994) in: In Situ Remediation: Scientific Basis for Current and Future Technologies (Gee, G. and Wing, R., Eds.), pp. 151-166. Battelle Press, Columbus, OH.
23. Fredrickson, J.K., Li, S.W., Brockman, F.J., Haldeman, D.L., Amy, P.S. and Balkwill, D.L. (1995) Time-dependent changes in viable numbers and activities of aerobic heterotrophic bacteria in subsurface samples. J. Microbiol. Methods 21, 253-265.
24. Haldeman, D.L., Amy, P.S., Ringelberg, D., White, D.C., Garen, R.E. and Ghiorse, W.C. (1995) Microbial growth and resuscitation alter community structure after perturbation. FEMS Microb. Ecol. 17, 27-38.
25. Haldeman, D.L., Amy, P.S., White, D.C. and Ringelberg, D.B. (1994) Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C. Appl. Environ. Microbiol. 60, 2697-2703.
26. West, A.W., Ross, D.J. and Cowling, J.C. (1986) Changes in microbial C, N, P and ATP contents, numbers and respiration on storage of soil. Soil Biol. Biochem. 18, 141-148.
27. Ross, D.J., Tate, K.R., Cairns, A. and Meyrick, K.F. (1980) Influence of storage on soil microbial biomass estimated by three biochemical procedures. Soil Biol. Biochem. 12, 369-374.
28. Fredrickson, J.K. et al. (1995) Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long-term microbial survival. Mol. Ecol. 4, 619-626.
29. Ghiorse, W.C. and Balkwill, D.L. (1983) Enumeration and morphological characterization of bacteria indigenous to subsurface environments. Dev. Ind. Microbiol. 24, 213-223.
30. Sinclair, J.L. and Ghiorse, W.C. (1989) Distribution of aerobic bacteria, protozoa, algae, and fungi in deep subsurface sediments. Geomicrobiol. J. 7, 15-32.
31. Chandler, D.P., Brockman, F.J. and Fredrickson, J.K. (1996) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. (in press).
32. Xia, X., Bollinger, J. and Ogram, A. (1995) Molecular genetic response of three soil microbial communities to the application of 2,4-D. Mol. Ecol. 4, 17-28.
33. Lane, D.J. (1991) in: Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 115-147. John Wiley and Sons Ltd., New York.
34. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
35. Schmidt, T.M., Pace, B. and Pace, N.R. (1992) Detection of DNA contamination in Taq polymerase. BioTechniques 11, 176-177.
36. Rochelle, P.A., Weightman, A.J. and Fry, J.C. (1992) DNase I treatment of Taq DNA polymerase for complete PCR decontamination. BioTechniques 13, 520.
37. Lee, S.Y., Bollinger, J., Bezdicek, D. and Ogram, A. (1996) Estimation of numbers of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62, 3787-3793.
38. Brockman, F.J. et al. (1994) Nucleic acid technology report for the in situ bioremediation demonstration (methane biostimulation) of the Savannah River Integrated Demonstration project. Pacific Northwest National Laboratory, PNL-SA10758.
39. Ward, D.M., Bateson, M.M., Weller, R. and Ruff-Roberts, A.L. (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12, 219-286.
40. Moyer, C.L., Tiedje, J.M., Dobbs, F.C. and Karl, D.M. (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62, 2501-2507.
41. Farrelly, V., Rainey, F.A. and Stackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61, 2798-2801.
42. Suzuki, M.T. and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625-630.
43. Mutter, G.L. and Boynton, K.A. (1995) PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies. Nucleic Acids Res. 23, 1411-1418.
44. Walsh, P.S., Erlich, H.A. and Higuchi, R. (1992) Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1, 241-250.
45. Tebbe, C.C. and Vahjen, W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast. Appl. Environ. Microbiol. 59, 2657-2665.
46. Robinson-Cox, J.F., Bateson, M.M. and Ward, D.M. (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61, 1240-1245.