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. 1997 Oct;63(10):3895–3901. doi: 10.1128/aem.63.10.3895-3901.1997

Seasonal changes in the relative abundance of uncultivated sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora.

J N Rooney-Varga 1, R Devereux 1, R S Evans 1, M E Hines 1
PMCID: PMC168699  PMID: 9327553

Abstract

Phylogenetic diversity and community composition of sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora were investigated. Uncultivated Desulfobacteriaceae family-related phylotypes were studied by selectively amplifying 16S rRNA gene fragments from DNA extracted from salt marsh rhizosphere samples. Two novel phylotypes were retrieved from rhizosphere samples, with A01 having 89.1% sequence similarity with Desulfococcus multivorans and 4D19 having 96.3% sequence similarity with Desulfosarcina variabilis. Additionally, six sequences that were extremely closely related to Desulfococcus multivorans (99% sequence similarity) were found. Reference RNAs containing sequences identical to corresponding cloned regions of A01 or 4D19 16S rRNA were synthesized via in vitro transcription and were used in subsequent quantitative membrane hybridization experiments. Oligonucleotide probes A01-183 and 4D19-189 were designed to specifically target these two novel phylotypes and were tested for target specificity against synthesized RNA and reference RNAs extracted from pure cultures. The newly designed probes were then used, together with eubacterial probes, to determine the relative abundances of the novel phylotypes in the salt marsh sediment and the rhizosphere. Mean relative abundances of A01-183 and 4D19-189 targets were 7.5 and 3.4%, respectively, suggesting that the target organisms of A01-183 and, to a lesser extent, of 4D19-189 play an important role in the salt marsh sediment and the Spartina rhizosphere. A seasonal trend of increased A01 relative abundance during the period of vegetative plant growth was evident, suggesting a close interaction between A01 and S. alterniflora.

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Selected References

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  1. Banta H. D., Gelijns A. C. The future and health care technology: implications of a system for early identification. World Health Stat Q. 1994;47(3-4):140–148. [PubMed] [Google Scholar]
  2. Borneman J., Skroch P. W., O'Sullivan K. M., Palus J. A., Rumjanek N. G., Jansen J. L., Nienhuis J., Triplett E. W. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol. 1996 Jun;62(6):1935–1943. doi: 10.1128/aem.62.6.1935-1943.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Braun-Howland E. B., Vescio P. A., Nierzwicki-Bauer S. A. Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates. Appl Environ Microbiol. 1993 Oct;59(10):3219–3224. doi: 10.1128/aem.59.10.3219-3224.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dacey J. W., Howes B. L. Water uptake by roots controls water table movement and sediment oxidation in short spartina marsh. Science. 1984 May 4;224(4648):487–489. doi: 10.1126/science.224.4648.487. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Devereux R., He S. H., Doyle C. L., Orkland S., Stahl D. A., LeGall J., Whitman W. B. Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. J Bacteriol. 1990 Jul;172(7):3609–3619. doi: 10.1128/jb.172.7.3609-3619.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Devereux R., Mundfrom G. W. A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment. Appl Environ Microbiol. 1994 Sep;60(9):3437–3439. doi: 10.1128/aem.60.9.3437-3439.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Devereux R, Hines ME, Stahl DA. S Cycling: Characterization of Natural Communities of Sulfate-Reducing Bacteria by 16S rRNA Sequence Comparisons. Microb Ecol. 1996 Nov;32(3):283–292. doi: 10.1007/BF00183063. [DOI] [PubMed] [Google Scholar]
  9. Hicks R. E., Amann R. I., Stahl D. A. Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl Environ Microbiol. 1992 Jul;58(7):2158–2163. doi: 10.1128/aem.58.7.2158-2163.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Holben W. E., Harris D. DNA-based monitoring of total bacterial community structure in environmental samples. Mol Ecol. 1995 Oct;4(5):627–631. doi: 10.1111/j.1365-294x.1995.tb00263.x. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Moran M. A., Torsvik V. L., Torsvik T., Hodson R. E. Direct extraction and purification of rRNA for ecological studies. Appl Environ Microbiol. 1993 Mar;59(3):915–918. doi: 10.1128/aem.59.3.915-918.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Moré M. I., Herrick J. B., Silva M. C., Ghiorse W. C., Madsen E. L. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol. 1994 May;60(5):1572–1580. doi: 10.1128/aem.60.5.1572-1580.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Polz M. F., Cavanaugh C. M. A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl Environ Microbiol. 1997 Mar;63(3):1028–1033. doi: 10.1128/aem.63.3.1028-1033.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Spring S., Amann R., Ludwig W., Schleifer K. H., van Gemerden H., Petersen N. Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl Environ Microbiol. 1993 Aug;59(8):2397–2403. doi: 10.1128/aem.59.8.2397-2403.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Telang A. J., Voordouw G., Ebert S., Sifeldeen N., Foght J. M., Fedorak P. M., Westlake D. W. Characterization of the diversity of sulfate-reducing bacteria in soil and mining waste water environments by nucleic acid hybridization techniques. Can J Microbiol. 1994 Nov;40(11):955–964. doi: 10.1139/m94-152. [DOI] [PubMed] [Google Scholar]
  18. Torsvik V., Goksøyr J., Daae F. L. High diversity in DNA of soil bacteria. Appl Environ Microbiol. 1990 Mar;56(3):782–787. doi: 10.1128/aem.56.3.782-787.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697–703. doi: 10.1128/jb.173.2.697-703.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

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