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. 1997 Apr;63(4):1498–1504. doi: 10.1128/aem.63.4.1498-1504.1997

Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.

N K Fry 1, J K Fredrickson 1, S Fishbain 1, M Wagner 1, D A Stahl 1
PMCID: PMC168444  PMID: 9097447

Abstract

Microbial communities of two deep (1,270 and 316 m) alkaline (pH 9.94 and 8.05), anaerobic (Eh, -137 and -27 mV) aquifers were characterized by rRNA-based analyses. Both aquifers, the Grande Ronde (GR) and Priest rapids (PR) formations, are located within the Columbia River Basalt Group in south-central Washington, and sulfidogenesis and methanogenesis characterize the GR and PR formations, respectively. RNA was extracted from microorganisms collected from groundwater by ultrafiltration through hollow-fiber membranes and hybridized to taxon-specific oligonucleotide probes. Of the three domains, Bacteria dominated both communities, making up to 92.0 and 64.4% of the total rRNA from the GR and PR formations, respectively. Eucarya comprised 5.7 and 14.4%, and Archaea comprised 1.8% and 2.5%, respectively. The gram-positive target group was found in both aquifers, 11.7% in GR and 7.6% in PR. Two probes were used to target sulfate- and/or metal-reducing bacteria within the delta subclass of Proteobacteria. The Desulfobacter groups was present (0.3%) only in the high-sulfate groundwater (GR). However, comparable hybridization to a probe selective for the desulfovibrios and some metal-reducing bacteria was found in both aquifers, 2.5 and 2.9% from the GR and PR formations, respectively. Selective PCR amplification and sequencing of the desulfovibrio/metal-reducing group revealed a predominance of desulfovibrios in both systems (17 of 20 clones), suggesting that their environmental distribution is not restricted by sulfate availability.

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Selected References

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  1. Alm E. W., Oerther D. B., Larsen N., Stahl D. A., Raskin L. The oligonucleotide probe database. Appl Environ Microbiol. 1996 Oct;62(10):3557–3559. doi: 10.1128/aem.62.10.3557-3559.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amann R. I., Binder B. J., Olson R. J., Chisholm S. W., Devereux R., Stahl D. A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990 Jun;56(6):1919–1925. doi: 10.1128/aem.56.6.1919-1925.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Amann R. I., Krumholz L., Stahl D. A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol. 1990 Feb;172(2):762–770. doi: 10.1128/jb.172.2.762-770.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Boom R., Sol C. J., Salimans M. M., Jansen C. L., Wertheim-van Dillen P. M., van der Noordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990 Mar;28(3):495–503. doi: 10.1128/jcm.28.3.495-503.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boone D. R., Liu Y., Zhao Z. J., Balkwill D. L., Drake G. R., Stevens T. O., Aldrich H. C. Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int J Syst Bacteriol. 1995 Jul;45(3):441–448. doi: 10.1099/00207713-45-3-441. [DOI] [PubMed] [Google Scholar]
  6. Bryant M. P., Campbell L. L., Reddy C. A., Crabill M. R. Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. Appl Environ Microbiol. 1977 May;33(5):1162–1169. doi: 10.1128/aem.33.5.1162-1169.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Devereux R., Delaney M., Widdel F., Stahl D. A. Natural relationships among sulfate-reducing eubacteria. J Bacteriol. 1989 Dec;171(12):6689–6695. doi: 10.1128/jb.171.12.6689-6695.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Flärdh K., Cohen P. S., Kjelleberg S. Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain CCUG 15956. J Bacteriol. 1992 Nov;174(21):6780–6788. doi: 10.1128/jb.174.21.6780-6788.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fredrickson J. K., Balkwill D. L., Drake G. R., Romine M. F., Ringelberg D. B., White D. C. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl Environ Microbiol. 1995 May;61(5):1917–1922. doi: 10.1128/aem.61.5.1917-1922.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ghiorse W. C., Wilson J. T. Microbial ecology of the terrestrial subsurface. Adv Appl Microbiol. 1988;33:107–172. doi: 10.1016/s0065-2164(08)70206-5. [DOI] [PubMed] [Google Scholar]
  11. Harvey R. W., George L. H. Growth determinations for unattached bacteria in a contaminated aquifer. Appl Environ Microbiol. 1987 Dec;53(12):2992–2996. doi: 10.1128/aem.53.12.2992-2996.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Harvey R. W., Smith R. L., George L. Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., aquifer. Appl Environ Microbiol. 1984 Dec;48(6):1197–1202. doi: 10.1128/aem.48.6.1197-1202.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kane M. D., Poulsen L. K., Stahl D. A. Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl Environ Microbiol. 1993 Mar;59(3):682–686. doi: 10.1128/aem.59.3.682-686.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kemp P. F., Lee S., Laroche J. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl Environ Microbiol. 1993 Aug;59(8):2594–2601. doi: 10.1128/aem.59.8.2594-2601.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kieft T. L., Fredrickson J. K., McKinley J. P., Bjornstad B. N., Rawson S. A., Phelps T. J., Brockman F. J., Pfiffner S. M. Microbiological Comparisons within and across Contiguous Lacustrine, Paleosol, and Fluvial Subsurface Sediments. Appl Environ Microbiol. 1995 Feb;61(2):749–757. doi: 10.1128/aem.61.2.749-757.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lin C., Stahl D. A. Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations. Appl Environ Microbiol. 1995 Apr;61(4):1348–1351. doi: 10.1128/aem.61.4.1348-1351.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lonergan D. J., Jenter H. L., Coates J. D., Phillips E. J., Schmidt T. M., Lovley D. R. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. J Bacteriol. 1996 Apr;178(8):2402–2408. doi: 10.1128/jb.178.8.2402-2408.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ogram A., Sun W., Brockman F. J., Fredrickson J. K. Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl Environ Microbiol. 1995 Feb;61(2):763–768. doi: 10.1128/aem.61.2.763-768.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Olsen G. J., Woese C. R., Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol. 1994 Jan;176(1):1–6. doi: 10.1128/jb.176.1.1-6.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pedersen K., Arlinger J., Hallbeck L., Pettersson C. Diversity and distribution of subterranean bacteria in groundwater at Oklo in Gabon, Africa, as determined by 16S rRNA gene sequencing. Mol Ecol. 1996 Jun;5(3):427–436. doi: 10.1111/j.1365-294x.1996.tb00332.x. [DOI] [PubMed] [Google Scholar]
  22. Poulsen L. K., Ballard G., Stahl D. A. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol. 1993 May;59(5):1354–1360. doi: 10.1128/aem.59.5.1354-1360.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Raskin L., Rittmann B. E., Stahl D. A. Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl Environ Microbiol. 1996 Oct;62(10):3847–3857. doi: 10.1128/aem.62.10.3847-3857.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Raskin L., Stromley J. M., Rittmann B. E., Stahl D. A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol. 1994 Apr;60(4):1232–1240. doi: 10.1128/aem.60.4.1232-1240.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Redburn A. C., Patel B. K. Desulfovibrio longreachii sp. nov., a sulfate-reducing bacterium isolated from the Great Artesian Basin of Australia. FEMS Microbiol Lett. 1994 Jan 1;115(1):33–38. doi: 10.1111/j.1574-6968.1994.tb06610.x. [DOI] [PubMed] [Google Scholar]
  26. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Stahl D. A., Flesher B., Mansfield H. R., Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol. 1988 May;54(5):1079–1084. doi: 10.1128/aem.54.5.1079-1084.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Van de Peer Y., Van den Broeck I., De Rijk P., De Wachter R. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 1994 Sep;22(17):3488–3494. doi: 10.1093/nar/22.17.3488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Zheng D., Alm E. W., Stahl D. A., Raskin L. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol. 1996 Dec;62(12):4504–4513. doi: 10.1128/aem.62.12.4504-4513.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]

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