Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate- reducing bacteria from diverse European sediments

Applied and Environmental Microbiology

Volumn 64, Issue 12, 1998, Pages 4846-4856

  Straub, Kristina L ^a   Buchholz Cleven, Berit E E ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FERROUS ION;

ANAEROBIC METABOLISM; ARTICLE; BACTERIAL COUNT; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CELL VIABILITY; EUROPE; GEL ELECTROPHORESIS; IN SITU HYBRIDIZATION; IRON METABOLISM; NONHUMAN; OLIGONUCLEOTIDE PROBE; OXIDATION; PHOTOTROPHIC BACTERIUM; SEDIMENT; STRAIN DIFFERENCE;

BACTERIA (MICROORGANISMS); PHOTOBACTERIA; POSIBACTERIA;

EID: 0031736825     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.12.4846-4856.1998     Document Type: Article

References (45)

1. 2+-oxidizing protein from Leptothrix discophora SS-1. J. Bacteriol. 169:1279-1285.
2. Alfreider, A., J. Pernthaler, R. I. Amann, B. Sattler, F.-O. Glöckner, A. Wille, and R. Psenner. 1996. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl. Environ. Microbiol. 62:2138-2144.
3. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
4. Amann, R., J. Snaidr, M. Wagner, W. Ludwig, and K.-H. Schleifer. 1996. In situ visualization of high genetic diversity in a natural microvial community. J. Bacteriol. 178:3496-3500.
5. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, 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.
6. 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.
7. 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.
8. Boogerd, F. C., and J. P. M. de Vrind. 1987. Manganese oxidation by Leptothrix discophora. J. Bacteriol. 169:489-494.
9. Brosius, J., T. L. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
10. Buchholz-Cleven, B. E. E., B. Rattunde, and K. L. Straub. 1997. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20:301-309.
11. Buresh, R. J., and J. T. Moraghan. 1976. Chemical reduction of nitrate by ferrous iron. J. Environ. Qual. 5:320-325.
12. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science 243:1360-1363.
13. de Man, J. C. 1975. The probability of most probable numbers. Eur. J. Appl. Microbiol. 1:67-78.
14. 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.
15. Dunbar, J., S. White, and L. Forney. 1997. Genetic diversity through the looking glass: effect of enrichment bias. Appl. Environ. Microbiol. 63:1326-1331.
16. Epstein, S. S., and J. Rossel. 1995. Enumeration of sandy sediment bacteria: search for optimal protocol. Mar. Ecol. Prog. Ser. 117:289-298.
17. Fachgruppe Wasserchemie, G. D. C. 1991. Deutsche Einheitsverfahren zur Wasser-, Abwasser-und Schlamm-Untersuchung, vol. Bd. II,E1. VCH, Weinheim, Germany.
18. Garrels, R. M., and C. L. Christ. 1965. Solutions, minerals and equilibria. Harper & Row, New York, N.Y.
19. Greenberg, A. E., L. S. Clesceri, and A. D. Eaton (ed.). 1992. Standard methods for the examination of water and wastewater. American Public Health Association, Washington, D.C.
20. 2+ at neutral pH under anoxic conditions. Arch. Microbiol. 166:308-314.
21. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, United Kingdom.
22. Lovley, D. R., and E. J. P. Phillips. 1987. Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl. Environ. Microbiol. 53:1536-1540.
23. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22:3485-3487.
24. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.-H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
25. Mobarry, B. K., M. Wagner, V. Urbain, B. Rittmann, and D. A. Stahl. 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62:2156-2162.
26. Moeslund, L., B. Thamdrup, and B. B. Jørgensen. 1994. Sulfur and iron cycling in a coastal sediment: radiotracer studies and seasonal dynamics. Biogeochemistry 27:129-152.
27. Moraghan, J. T., and R. J. Buresh. 1976. Chemical reduction of nitrite and nitrous oxide by ferrous iron. Soil Sci. Soc. Am. J. 41:47-50.
28. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676-2680.
29. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
30. Muyzer, G., S. Hottenträger, A. Teske, and C. Wawer. 1996. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA. A new molecular approach to analyze the genetic diversity of mixed microbial communities, p. 3.4.4:1-3.4.4:23. In A. D. L. Akkermans, J. D. Van Elsas, and F. J. De Bruijn (ed.), Molecular microbial ecology manual, 2nd ed. Kluwer Academic Publishers, Dordrecht, The Netherlands.
31. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
32. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic flora. Limnol. Oceanogr. 25:943-948.
33. Poulsen, L. K., G. Ballard, and D. A. Stahl. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59:1354-1360.
34. Rabus, R., and F. Widdel. 1995. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch. Microbiol. 163:96-103.
35. Ramsing, N. B., H. Fossing, T. G. Ferdelman, F. Andersen, and B. Thamdrup. 1996. Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl. Environ. Microbiol. 62:1391-1404.
36. Sheffield, V. C., D. R. Cox, L. S. Lerman, and R. M. Myers. 1989. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86:232-236.
37. Straub, K. L. Unpublished data.
38. Straub, K. L., M. Benz, B. Schink, and F. Widdel. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. 62:1458-1460.
39. 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.
40. Thauer, R. K., K. Jungermann, and K. Decker. 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41:100-180.
41. Wallner, G., R. Erhart, and R. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61: 1859-1866.
42. Ward, D. M., C. M. Santegoeds, S. C. Nold, N. B. Ramsing, M. J. Ferris, and M. M. Bateson. 1997. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie Leeuwenhoek 71:143-150.
43. Widdel, F., and F. Bak. 1992. Gram-negative mesophilic sulfate-reducing bacteria, p. 3352-3378. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer, Berlin, Germany.
44. Widdel, F., S. Schnell, S. Heising, A. Ehrenreich, B. Assmus, and B. Schink. 1993. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362:834-836.
45. Zhou, J., A. M. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.