Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA

Applied and Environmental Microbiology

Volumn 65, Issue 4, 1999, Pages 1516-1523

  Edgcomb, Virginia P ^a,c   McDonald, John H ^a   Devereux, Richard ^b   Smith, David W ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HUMIC ACID; RIBOSOME DNA; RNA 16S;

BACTERIUM; DNA; POPULATION ESTIMATION; SALTMARSH; SEDIMENT;

ARTICLE; BACTERIAL COUNT; DESULFOVIBRIO; DNA PROBE; ECOSYSTEM; HYBRIDIZATION; MEMBRANE BINDING; NONHUMAN; SEDIMENT;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO; NEGIBACTERIA;

EID: 0032933224     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.4.1516-1523.1999     Document Type: Article

References (43)

1. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1994. Identification of uncultured bacteria: a challenging task for molecular taxonomists. ASM News 60:360-365.
3. Amann, R. I., J. Stromley, R. Devereux, R. Key, and D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58:614-623.
4. Amann, R. I., B. Binder, S. W. Chisholm, R. Olsen, R. Devereux, and D. A. Stahl, 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
5. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
6. Atlas, R. M., G. Sayler, R. S. Burlage, and A. K. Bej. 1992. Molecular approaches for environmental monitoring of microorganisms. BioTechniques 12:706-717.
7. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. K. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
8. Brace, K. D., W. D. Hiorns, J. L. Hobman, A. M. Osborn, P. Strike, and D. A. Ritchie. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl. Environ. Microbiol. 58:3413-3416.
9. Dairy, G. 1997. Nature's services - societal dependence on natural ecosystems, p. 37-38. Island Press, Washington, D.C.
10. Delgado, S., and J. Wall (Department of Biochemistry, University of Missouri - Columbia). Isolation of genomic DNA from Desulfovibrio desulfuricans. Personal communication.
11. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
12. Devereux, R., S. G. Willis, and M. E. Hines. 1997. Genome sizes of Desulfovibrio desulfuricans, Desulfovibrio vulgaris, and Desulfobulbus proprionicus estimated by pulsed-field gel electrophoresis of linearized chromosomal DNA. Curr. Microbiol. 34:337-339.
13. Devereux, R., M. E. Hines, and D. A. Stahl. 1996. S cycling: characterization of natural communities of sulfate-reducing bacteria by 16S rRNA sequence comparisons. Microb. Ecol. 32:283-292.
14. Devereux, R., and D. A. Stahl. 1993. Phylogeny of sulfate-reducing bacteria and a perspective for analyzing their natural communities, p. 131-159. In J. M. Odom and R. Singleton (ed.), The sulfate-reducing bacteria: contemporary perspectives. Springer-Verlag, Inc., New York, N.Y.
15. Devereux, R., M. D. Kane, J. Winfrey, and D. A. Stahl. 1992. Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15:601-609.
16. Dicker, H. J., and D. W. Smith. 1980. Enumeration and relative importance of acetylene-reducing (nitrogen-fixing) bacteria in a Delaware salt marsh. Appl. Environ. Microbiol. 39:1019-1025.
17. Family, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rm gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
18. Hahn, D., R. I. Amann, W. Ludwig, A. D. L. Akkermans, and K.-H. Schleifer. 1992. Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labeled oligonucleotides. J. Gen. Microbiol. 138:879-887.
19. Holben, W. E., and D. Harris. 1995. DNA-based monitoring of total bacterial community structure in environmental samples. Mol. Ecol. 4:627-631.
20. Holben, W. E., J. K. Janson, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe methods for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
21. Jacobsen, C. S., and O. F. Rasmussen. 1992. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl. Environ. Microbiol. 58:2458-2462.
22. Kane, M. D., L. K. Poulsen, and D. A. Stahl. 1993 Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl. Environ. Microbiol. 59:682-686.
23. Kemp, P. F., S. Lee, and J. LaRoche. 1993. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59:2594-2601.
24. Ketcham, R. B. 1981. Seasonal dynamics of lithotrophic and heterotrophic bacteria in salt marsh soils. M.S. thesis. University of Delaware, Newark.
25. Lovell, C. R., and Y. Piceno. 1994. Purification of DNA from estuarine sediments. J. Microbiol. Methods 10:161-174.
26. MacGregor, B. J., D. P. Moser, E. W. Alm, K. H. Nealson, and D. A. Stahl. 1997. Crenarchaeota in Lake Michigan sediment. Appl. Environ. Microbiol. 63:1178-1181.
27. Moller, S., A. R. Pedersen, L. K. Poulsen, E. Arvin, and S. Molin. 1996. Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl. Environ. Microbiol. 62:4632-4640.
28. Nedelman, J., P. Heagerty, and C. Lawrence. 1992. Quantitative PCR: procedures and precisions. Bull. Math. Biol. 54:477-502.
29. Odenyo, A. A., R. I. Mackie, D. A. Stahl, and B. A. White. 1994. The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production. Appl. Environ. Microbiol. 60:3688-3696.
30. Ogram, A., G. S. Sayler, and T. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
31. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241-1248.
32. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
33. Somerville, C. C., I. T. Knight, W. L. Straube, and R. R. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55:548-554.
34. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
35. Szostak, J. W., J. I. Stiles, B.-K. Tye, P. Chiu, F. Sherman, and R. Wu. 1979. Hybridization with synthetic oligonucleotide probes. Methods Enzymol. 68: 419-427.
36. Teske, A., C. Wawer, G. Muyzer, and N. B. Ramsing. 1996. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1405-1415.
37. Torsvik, V., K. Salte, R. Sorheim, and J. Goksoyr. 1990. Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl. Environ. Microbiol. 56:776-781.
38. Tsai, Y.-L., and B. Olson. 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58:754-757.
39. Tsai, Y.-L., and B. H. Olson. 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58:2292-2295.
40. Tsai, Y.-L., and B. H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
41. Wall, J. D. 1993. Characterization of a small plasmid from Desulfovibrio desulfuricans and its use for shuttle vector construction. J. Bacteriol. 175: 4121-4128.
42. Ward, D. M., M. M. Bateson, R. Weller, and A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:219-286.
43. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.