1887

Abstract

Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy’s Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to . The other two strains appeared to be most closely related to . The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of , and genera recently separated from , such as . Some of the subsurface strains were phylogenetically closely related to certain species of (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of .

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2000-06-01
2019-12-13
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References

  1. Amy, P. S., Haldeman, D. L., Ringelberg, D., Hall, D. H. & Russell, C. ( 1992; ). Comparison of identification systems for classification of bacteria isolated from water and endolithic habitats within the deep subsurface. Appl Environ Microbiol 58, 3367-3373.
    [Google Scholar]
  2. Applied Biosystems (1992). Taq DyeDeoxy Terminator Cycle Sequencing Kit User Bulletin no. 901497, Revision E. Foster City, CA: Applied Biosystems.
  3. Applied Biosystems (1994). Autoassembler DNA Sequence Assembly Software User Manual no. 903226, Revision A. Foster City, CA: Applied Biosystems.
  4. Balkwill, D. L. ( 1989; ). Numbers, diversity, and morphological characterization of aerobic, chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina. Geomicrobiol J 7, 33-51.[CrossRef]
    [Google Scholar]
  5. Balkwill, D. L. ( 1993; ). DOE makes subsurface cultures available. ASM News 59, 504-506.
    [Google Scholar]
  6. Balkwill, D. L. & Boone, D. R. ( 1997; ). Identity and diversity of microorganisms cultured from subsurface environments. In The Microbiology of the Terrestrial Deep Subsurface, pp. 105-117. Edited by P. S. Amy & D. L. Haldeman. New York: Lewis Publishers.
  7. Balkwill, D. L. & Ghiorse, W. C. ( 1985; ). Characterization of subsurface bacteria associated with two shallow aquifers in Oklahoma. Appl Environ Microbiol 50, 580-588.
    [Google Scholar]
  8. Balkwill, D. L., Fredrickson, J. K. & 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, 1058-1065.
    [Google Scholar]
  9. Balkwill, D. L., Reeves, R. H., Drake, G. R., Reeves, J. Y., Crocker, F. H., King, M. B. & Boone, D. R. ( 1997; ). Phylogenetic characterization of bacteria in the subsurface microbial culture collection. FEMS Microbiol Rev 20, 201-216.[CrossRef]
    [Google Scholar]
  10. Boivin-Jahns, V., Bianchi, A., Ruimy, R., Garcin, J., Daumas, S. & Christen, R. ( 1995; ). Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl Environ Microbiol 61, 3400-3406.
    [Google Scholar]
  11. Boone, D. R., Liu, Y., Zhao, Z.-J., Balkwill, D. L., Drake, G. R., Stevens, T. O. & Aldrich, H. C. ( 1995; ). Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int J Syst Bacteriol 45, 441-448.[CrossRef]
    [Google Scholar]
  12. Boquet, E., Boronat, A. & Ramos-Cormenzana, A. ( 1973; ). Production of calcite (calcium carbonate) crystals by soil bacteria is a general phenomenon. Nature 246, 527-528.[CrossRef]
    [Google Scholar]
  13. Brockman, F. J., Kieft, T. L., Fredrickson, J. K., Bjornstad, B. N., Li, S. W., Spangenberg, W. & Long, P. E. ( 1992; ). Microbiology of vadose zone paleosols in south-central Washington State. Microb Ecol 23, 279-301.[CrossRef]
    [Google Scholar]
  14. Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. R. ( 1979; ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75, 4801-4805.
    [Google Scholar]
  15. Chandler, D. P., Li, S.-M., Spadoni, C. M., Drake, G. R., Balkwill, D. L., Fredrickson, J. K. & Brockman, F. J. ( 1997; ). A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiol Ecol 23, 131-144.[CrossRef]
    [Google Scholar]
  16. Colwell, F. S., Stormberg, G. J., Phelps, T. J. & 11 other authors ( 1992; ). Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization. J Microbiol Methods 15, 279–292.[CrossRef]
    [Google Scholar]
  17. Cote, R. J. & Gherna, R. L. ( 1994; ). Nutritional media. In Methods for General and Molecular Bacteriology, pp. 155-178. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  18. Cure, G. L. & Keddie, R. M. ( 1973; ). Methods for morphological examination of aerobic coryneform bacteria. In Sampling – Microbiological Monitoring of Environments (Society for Applied Bacteriology Technical Series 7), pp. 123-135. Edited by R. G. Board & D. N. Lovelock. London: Academic Press.
  19. DeSoete, G. ( 1983; ). A least squares algorithm for fitting additive trees to proximity data. Psychometrica 48, 621-626.[CrossRef]
    [Google Scholar]
  20. Difco (1984). Difco Manual: Dehydrated Culture Media and Reagents for Microbiology, 10th edn. Detroit: Difco Laboratories.
  21. Ekendahl, S., Arlinger, J., Ståhl, F. & Pedersen, K. ( 1994; ). Characterization of attached bacterial populations in deep granitic groundwater from the Stripa research mine by 16S-rRNA gene sequencing and scanning electron microscopy. Microbiology 140, 1575-1583.[CrossRef]
    [Google Scholar]
  22. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.[CrossRef]
    [Google Scholar]
  23. Felsenstein, J. (1993). phylip (Phylogeny Inference Package), version 3.5c. Seattle: University of Washington.
  24. Fitch, W. M. & Margoliash, E. ( 1967; ). Construction of phylogenetic trees. Science 155, 279-284.[CrossRef]
    [Google Scholar]
  25. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P.Jr ( 1992; ). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166-170.[CrossRef]
    [Google Scholar]
  26. Fredrickson, J. K., Balkwill, D. L., Zachara, J. M., Li, S. W., Brockman, F. J. & Simmons, M. A. ( 1991; ). Physiological testing and distribution of heterotrophic bacteria in deep Cretaceous sediments of the Atlantic Coastal Plain. Appl Environ Microbiol 57, 402-411.
    [Google Scholar]
  27. Fredrickson, J. K., Brockman, F. J., Bjornstad, B. N. & 7 other authors ( 1993; ). Microbiological characteristics of pristine and contaminated deep vadose sediments from an arid region. Geomicrobiol J 11, 95–107.[CrossRef]
    [Google Scholar]
  28. Fredrickson, J. K., McKinley, J. P., Nierzwicki-Bauer, S. A., White, D. C., Ringelberg, D. B., Rawson, S. A., Li, S., Brockman, F. J. & Bjornstad, B. N. ( 1995; ). Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long-term microbial survival. Mol Ecol 4, 619-626.[CrossRef]
    [Google Scholar]
  29. Ghiorse, W. C. & Wilson, J. T. ( 1988; ). Microbial ecology of the terrestrial subsurface. Adv Appl Microbiol 33, 107-272.
    [Google Scholar]
  30. Hagedorn, C. & Holt, J. G. ( 1975; ). A nutritional and taxonomic survey of Arthrobacter soil isolates. Can J Microbiol 21, 353-361.[CrossRef]
    [Google Scholar]
  31. Haldeman, D. L. & Amy, P. S. ( 1993; ). Bacterial heterogeneity in deep subsurface tunnels at Ranier Mesa, Nevada Test Site. Microb Ecol 25, 183-194.
    [Google Scholar]
  32. Haldeman, D. L., Amy, P. S., Ringelberg, D. & White, D. C. ( 1993; ). Characterization of the microbiology within a 21 m3 section of rock from the deep subsurface. Microb Ecol 26, 145-159.
    [Google Scholar]
  33. Johnson, J. L. ( 1981; ). Genetic characterization. In Manual of Methods for General Bacteriology, pp. 450-472. Edited by P. Gerhardt, R. G. E. Murray, R. W. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
  34. Jukes, T. H. & Cantor, C. R. ( 1963; ). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
  35. Keddie, R. M., Collins, D. & Jones, D. ( 1986; ). Genus Arthrobacter. In Bergey’s Manual of Systematic Bacteriology, pp. 1288-1301. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  36. Kieft, T. L., Amy, P. S., Brockman, F. J., Fredrickson, J. K., Bjornstad, B. N. & Rosacker, L. L. ( 1993; ). Microbial abundance and activities in relation to water potential in the vadose zone of arid and semiarid sites. Microb Ecol 26, 59-78.[CrossRef]
    [Google Scholar]
  37. Kieft, T. L., Fredrickson, J. K., McKinley, J. P., Bjornstad, B. N., Rawson, S. A., Phelps, T. J., Brockman, F. J. & Pfiffner, S. M. ( 1995; ). Microbiological comparisons within and across contiguous lacustrine, paleosol, and fluvial subsurface sediments. Appl Environ Microbiol 61, 749-757.
    [Google Scholar]
  38. Koch, C., Rainey, F. A. & Stackebrandt, E. ( 1994; ). 16S rDNA studies on members of Arthrobacter and Micrococcus: an aid for their future taxonomic restructuring. FEMS Microbiol Lett 123, 167-172.[CrossRef]
    [Google Scholar]
  39. Koch, C., Schumann, P. & Stackebrandt, E. ( 1995; ). Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter. Int J Syst Bacteriol 45, 837-839.[CrossRef]
    [Google Scholar]
  40. Lane, D. J., Pace, G., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R. ( 1985; ). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82, 6955-6959.[CrossRef]
    [Google Scholar]
  41. McBride, L. J., Koepf, S. M., Gibbs, R. A., Salser, W., Mayrand, P. E., Hunkapiller, M. W. & Kronick, M. N. ( 1989; ). Automated DNA sequencing methods involving polymerase chain reaction. Clin Chem 35, 2196-2201.
    [Google Scholar]
  42. McKinley, J. P., Stevens, T. O., Fredrickson, J. K., Zachara, J. M., Colwell, F. S., Wagnon, K. B., Smith, S. C., Rawson, S. A. & Bjornstad, B. N. ( 1997; ). Biogeochemistry of anaerobic lacustrine and paleosol sediments within an aerobic unconfined aquifer. Geomicrobiol J 14, 23-39.[CrossRef]
    [Google Scholar]
  43. Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R. ( 1996; ). The ribosomal database project (RDP). Nucleic Acids Res 24, 82-85.[CrossRef]
    [Google Scholar]
  44. Pace, N. R., Stahl, D. A., Land, D. J. & Olsen, G. J. ( 1986; ). The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9, 1-55.
    [Google Scholar]
  45. Pedersen, K. & Ekendahl, S. ( 1990; ). Distribution and activity of bacteria in deep granitic groundwaters of southeastern Sweden. Microb Ecol 20, 37-52.[CrossRef]
    [Google Scholar]
  46. Pedersen, K. & Ekendahl, S. ( 1992; ). Assimilation of CO2 and introduced organic compounds by bacterial communities in groundwater from southeastern Sweden deep crystalline bedrock. Microb Ecol 23, 1-14.[CrossRef]
    [Google Scholar]
  47. Pedersen, K., Arlinger, J., Ekendahl, S. & Halbeck, L. ( 1996a; ). 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel of the Åspö hard rock laboratory, Sweden. FEMS Microbiol Ecol 19, 249-262.
    [Google Scholar]
  48. Pedersen, K., Arlinger, J., Hallbeck, L. & Pettersson, C. ( 1996b; ). Diversity and distribution of subterranean bacteria in groundwater at Oklo in Gabon, Africa, as determined by 16S rRNA gene sequencing. Mol Ecol 5, 427-436.[CrossRef]
    [Google Scholar]
  49. Phelps, T. J., Fliermans, C. B., Garland, T. R., Pfiffner, S. M. & White, D. C. ( 1989; ). Methods for recovery of deep terrestrial subsurface sediment for microbiological analyses. J Microbiol Methods 9, 15-27.[CrossRef]
    [Google Scholar]
  50. Reeves, R. H., Reeves, J. Y. & Balkwill, D. L. ( 1995; ). Strategies for phylogenetic characterization of subsurface bacteria. J Microbiol Methods 21, 235-251.[CrossRef]
    [Google Scholar]
  51. Russell, B. F., Phelps, T. J., Griffin, W. T. & Sargent, K. A. ( 1992; ). Procedures for sampling deep subsurface microbial communities in unconsolidated sediments. Ground Water Monit Rev 12, 96-104.[CrossRef]
    [Google Scholar]
  52. Rusterholtz, K. J. & Mallory, L. M. ( 1994; ). Density, activity, and diversity of bacteria indigenous to a karstic aquifer. Microb Ecol 28, 79-99.
    [Google Scholar]
  53. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  54. Sasser, M. (1990). Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. North Newark, DE: MIDI.
  55. Sperber, J. I. ( 1958; ). The incidence of apatite-solubilizing organisms in the rhizosphere and soil. Aust J Agric Res 9, 778-781.[CrossRef]
    [Google Scholar]
  56. Stackebrandt, E. & Fiedler, F. ( 1979; ). DNA–DNA homology studies among strains of Arthrobacter and Brevibacterium. Arch Microbiol 120, 289-295.[CrossRef]
    [Google Scholar]
  57. Stackebrandt, E., Fowler, V. J., Fiedler, F. & Heiler, H. ( 1983; ). Taxonomic studies on Arthrobacter nicotianae and related taxa: description of Arthrobacter uratoxydans sp. nov. and Arthrobacter sulfureus sp. nov. and reclassification of Brevibacterium protophormiae as Arthrobacter protophormiae comb. nov. Syst Appl Microbiol 4, 470-486.[CrossRef]
    [Google Scholar]
  58. Stackebrandt, E., Koch, C., Gvozdiak, O. & Schumann, P. ( 1995; ). Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45, 682-692.[CrossRef]
    [Google Scholar]
  59. Stevens, T. O. & Holbert, B. S. ( 1995; ). Variability and density-dependence of bacteria in terrestrial subsurface samples: implications for enumeration. J Microbiol Methods 21, 283-292.[CrossRef]
    [Google Scholar]
  60. Stevenson, I. L. ( 1967; ). Utilization of aromatic hydrocarbons by Arthrobacter spp. Can J Microbiol 13, 205-211.[CrossRef]
    [Google Scholar]
  61. Swofford, D. L. ( 2000; ). paup * 4.0, beta version 4a. Sunderland, MD: Sinauer Associates.
    [Google Scholar]
  62. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. ( 1991; ). 16S ribosomal RNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
    [Google Scholar]
  63. Woese, C. ( 1987; ). Bacterial evolution. Microbiol Rev 51, 221-271.
    [Google Scholar]
  64. Wollum, A. G.II ( 1982; ). Cultural methods for soil microorganisms. In Methods of Soil Analysis, Part 2: Chemical and Microbiological Properties, pp. 781-782. Edited by A. L. Page. Madison, WI: American Society for Agronomy.
  65. Zheng, M. & Kellog, S. T. ( 1994; ). Analysis of bacterial populations in a basalt aquifer. Can J Microbiol 40, 944-954.[CrossRef]
    [Google Scholar]
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