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References

  • 1
    Balkwill, D.L., Fredrickson, J.K. and Thomas, J.M. (1989) Vertical and horizontal variations in the physiological diversity of the aerobic chemoheterotrophic bacterial microflora in deep southeast coastal plain subsurface sediments. Appl. Environ. Microbiol. 55, 10581065.
  • 2
    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, 5366.
  • 3
    Fredrickson, J.K. et al. (1993) Microbiological characteristics of pristine and contaminated deep vadose sediments from an arid region. Geomicrobiol. J. 11, 95107.
  • 4
    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, 279301.
  • 5
    Fredrickson, J.K. et al. (1995) Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long-term microbial survival. Mol. Ecol. 4, 619626.
  • 6
    Haldeman, D.L., Pitonzo, B.J., Story, S.P. and Amy, P.S. (1994) Comparison of the microbiota recovered from surface and deep subsurface rock, water, and soil along an elevational gradient. Geomicrobiol. J. 12, 99111.
  • 7
    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.
  • 8
    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, 219286.
  • 9
    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, 155.
  • 10
    Fuhrman, J.A., McCallum, K. and Davis, A.A. (1992) Novel major archaebacterial group from marine plankton. Nature 356, 148149.
  • 11
    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, 16091613.
  • 12
    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, 50725078.
  • 13
    Liesack, W. and Stackebrandt, E. (1992) Unculturable microbes detected by molecular sequences and probes. Biodiversity Conservation 1, 250262.
  • 14
    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, 625630.
  • 15
    Reysenbach, A.-L., Giver, L.J., Wickham, G.S. and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58, 34173418.
  • 16
    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, 27982801.
  • 17
    Chandler, D.P., Brockman, F.J. and Fredrickson, J.K. (1997) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6, 475482.
  • 18
    Balkwill, D.L. (1993) DOE makes subsurface cultures available. ASM News 59, 504506.
  • 19
    Chandler, D.P., Brockman, F.J. and Fredrickson, J.K. (1997) Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol. Rev. (in press).
  • 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, 749757.
  • 21
    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, 3352.
  • 22
    Stevens, T.O. (1995) Optimization of media for enumeration and isolation of aerobic heterotrophic bacteria from the deep terrestrial subsurface. J. Microbiol. Methods 21, 293303.
  • 23
    Ghiorse, W.C. and Balkwill, D.L. (1983) Enumeration and morphological characterization of bacteria indigenous to subsurface environments. Dev. Ind. Microbiol. 24, 213223.
  • 24
    Sinclair, J.L. and Ghiorse, W.C. (1989) Distribution of aerobic bacteria, protozoa, algae, and fungi in deep subsurface sediments. Geomicrobiol. J. 7, 1532.
  • 25
    Balkwill, D.L. et al. (1997) Taxonomic study of aromatic-degrading bacteria from deep terrestrial subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterrae sp. nov., and Sphingomonas stygialis sp. nov. Int. J. Syst. Bacteriol. 47, 191201.
  • 26
    Maidak, B.L., Larsen, N., McCaughey, M.J., Overbeek, R., Olsen, G.J., Fogel, K., Blandy, J. and Woese, C.R. (1994) The Ribosomal Database Project. Nucleic Acids Res. 22, 34853487.
  • 27
    Brockman, F.J., Li, S.W., Fredrickson, J.K., Ringelberg, D.B., Kieft, T.L., Spadoni, C.M., McKinley, J.P. and White, D.C. (1996) Post-sampling changes in microbial community structure and activity in a subsurface paleosol. Microb. Ecol. (submitted).
  • 28
    Haldeman, D.L. and Amy, P.S. (1993) Diversity within a colony morphotype: implications for ecological research. Appl. Environ. Microbiol. 59, 933935.
  • 29
    Brunk, C.F., Avaniss-Aghajani, E. and Brunk, C.A. (1996) A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl. Environ. Microbiol. 62, 872879.
  • 30
    Clayton, R.A., Sutton, G., Hinkle, P.S.J., Bult, C. and Fields, C. (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45, 595599.
  • 31
    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, 14111418.
  • 32
    Walsh, P.S., Erlich, H.A. and Higuchi, R. (1992) Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1, 241250.
  • 33
    Sarkar, G., Cassady, J., Bottema, C.D.K. and Sommer, S.S. (1990) Characterization of polymerase chain reaction amplification of specific alleles. Anal. Biochem. 186, 6468.
  • 34
    Chandler, D.P., Brockman, F.J. and Fredrickson, J.K. (1997) Molecular phylogeny of a deep subsurface microbial community. Microb. Ecol. (submitted).
  • 35
    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, 871879.
  • 36
    Ward, N., Rainey, F.A., Goebel, B. and Stackebrandt, E. (1995) In: Microbial Diversity and Ecosystem Function (Allsopp, D., Colwell, R.R. and Hawksworth, D.L., Eds.), pp. 89–110. CAB International.
  • 37
    Stackebrandt, E., Liesack, W. and Goebel, B.M. (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7, 232236.
  • 38
    Stahl, D.A. (1995) Application of phylogenetically based hybridization probes to microbial ecology. Mol. Ecol. 4, 535542.