Microbial community composition of wadden sea sediments as revealed by fluorescence in situ hybridization

Applied and Environmental Microbiology

Volumn 64, Issue 7, 1998, Pages 2691-2696

  Llobet Brossa, Enric ^a   Rosselló Mora, Ramon ^a   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY COMPOSITION; FLUORESCENCE; MICROBIAL COMMUNITY; SEDIMENT;

AQUATIC FLORA; ARTICLE; BACTERIAL FLORA; BACTERIUM IDENTIFICATION; FLAVOBACTERIUM; FLEXIBACTERACEAE; FLUORESCENCE IN SITU HYBRIDIZATION; NONHUMAN; SEA; SEDIMENT;

WADDEN SEA;

BACTERIA (MICROORGANISMS); CYTOPHAGA; FLAVOBACTERIUM; FLEXIBACTERACEAE;

EID: 0344765523     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.7.2691-2696.1998     Document Type: Article

References (51)

1. Amann, R. I., B. J. Binder, R. J. Olsen, 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.
2. 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.
3. Anguish, L. J., and W. C. Ghiorse. 1997. Computer-assisted laser scanning and video microscopy for analysis of Cryptosporidium parvum oocysts in soil, sediment, and feces. Appl. Environ. Microbiol. 63:724-733.
4. Bowman, J. P., S. A. McCammon, M. V. Brown, D. S. Nichols, and T. A. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:3068-3078.
5. Cammen, L. M. 1991. Annual bacterial production in relation to benthic microalgal production and sediment oxygen uptake in an intertidal sandflat and an intertidal mudflat. Mar. Ecol. Prog. Ser. 71:13-25.
6. Delille, D. 1995. Seasonal changes of subantarctic benthic bacterial communities. Hydrobiologia 310:45-57.
7. DeLong, E. F., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
8. DeLong, E. F., K. Y. Wu, B. B. Prézelin, and R. V. M. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697.
9. Devereux, R., M. R. Winfrey, J. Winfrey, and D. A. Stahl. 1996. Depth profile of sulfate-reducing bacterial ribosomal RNA and mercury methylation in an estuarine sediment. FEMS Microbiol. Ecol. 20:23-31.
10. Do, H. K., K. Kogure, and U. Simidu. 1990. Identification of deep-sea-sediment bacteria which produce tetrodotoxin. Appl. Environ. Microbiol. 56:1162-1163.
11. Fuhrman, J. A., and A. A. Davis. 1997. Widespread Archaea and novel bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar. Ecol. Prog. Ser. 150:275-285.
12. Fukui, M., G. Muyzer, A. Teske, B. Assmus, and F. Widdel (Max Planck Institut for Marine Microbiology, Bremen, Germany). 1998. Personal communication.
13. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
14. Glöckner, F. O., R. Amann, A. Alfreider, J. Pernthaler, R. Psenner, K. Trebesius, and K.-H. Schleifer. 1996. An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst. Appl. Microbiol. 19:403-406.
15. Gonzalez, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
16. Gray, J. P., and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62:4049-4059.
17. Heyer, K., M. Engel, U. H. Brockmann, H.-J. Rick, C.-D. Dürselen, H. Hünnerfuss, U. Kammann, H. Steinhart, W. Kienz, M. Krause, L. Karbe, A. Faubel, and S. Regier. 1994. Local studies in the German Bight during winter/spring 1988/1989, p. 190-249. In J. Sündermann (ed.), Circulation and contaminant fluxes in the North Sea. Springer-Verlag, Berlin, Germany.
18. Holmes, B. 1991. The genera Flavobacterium, Sphingobacterium, and Weeksella, p. 3620-3630. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes. Springer-Verlag, Berlin, Germany.
19. Hyllerberg, J., and H. Riis-Vestergaard. 1984. Marine environments; the fate of detritus. Akademisk Forlag, Copenhagen, Denmark.
20. Jørgensen, B. B., and F. Bak. 1991. Pathways and microbiology of thiosulfate transformations and sulfate reduction in marine sediment (Kattegat, Denmark). Appl. Environ. Microbiol. 57:847-856.
21. Jørgensen, B. B., and N. P. Revsbech. 1989. Oxygen uptake, bacterial distribution, and carbon-nitrogen-sulfur cycling in sediments from the Baltic Sea-North Sea transition. Ophelia 31:29-49.
22. 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.
23. Meyer-Reil, L.-A. 1993. Mikrobielle besiedlung und Produktion, p. 38-81. In L.-A. Meyer-Reil and M. Köster (ed.), Mikrobiologie des Meeresbodens. Gustav Fischer Verlag, Jena, Germany.
24. Moran, M. A., L. T. Rutherford, and R. E. Hodson. 1995. Evidence for indigenous Streptomyces populations in a marine environment determined with a 16S rRNA probe. Appl. Environ. Microbiol. 61:3695-3700.
25. Moyer, C., F. C. Dobbs, and D. M. Karl. 1994. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60:871-879.
26. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
27. Neef, A. 1997. Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. Ph.D. thesis. Technical University of Munich, Munich, Germany.
28. Novitsky, J. A. 1990. Evidence for sedimenting particles as the origin of the microbial community in coastal marine sediment. Mar. Ecol. Prog. Ser. 60:161-167.
29. Ogram, A., W. Sun, F. J. Brockman, and J. K. Fredrickson. 1995. Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl. Environ. Microbiol. 61:763-768.
30. Parkes, R. J., B. A. Cragg, S. J. Bale, J. M. Getllff, K. Goodman, P. A. Rochelle, J. C. Fry, A. J. Weightman, and S. M. Harvey. 1994. Deep bacterial biosphere in Pacific Ocean sediments. Nature 371:410-413.
31. Pernthaler, J., A. Alfreider, T. Posch, S. Andreatta, and R. Psenner. 1997. In situ classification and image cytometry of pelagic bacterial from a high mountain lake (Gossenköllesee, Austria). Appl. Environ. Microbiol. 63:4778-4783.
32. 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.
33. Rappé, M. S., P. F. Kemp, and S. J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42:811-826.
34. Reisenbach, H. 1991. The order Cytophagales, p. 3631-3675. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer, (ed.), The prokaryotes. Springer-Verlag, Berlin, Germany.
35. Risatti, J. B., W. C. Capman, and D. A. Stahl. 1994. Community structure of a microbial mat: the phylogenetic dimension. Proc. Natl. Acad. Sci. USA 91:10173-10177.
36. Rochelle, P. A., B. A. Cragg, J. C. Fry, R. J. Parkes, and A. J. Weightman. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecol. 15:215-226.
37. Sageman, J. 1994. Saisonale variationen von porenwasserprofilen, nährstoffflüssen und reaktionen in intertidalen sedimenten des Weser ästuares. Ph.D. thesis. Bremen University, Bremen, Germany.
38. Sander, B. C., and J. Kalff. 1993. Factors controlling bacterial production in marine and freshwater sediments. Microb. Ecol. 26:79-99.
39. Sass, H., H. Cypionka, and H.-D. Babenzien. 1997. Vertical distribution of sulfate-reducing bacteria at the oxic-anoxic interface in sediments of the oligotrophic Lake Stechlin. FEMS Microbiol. Ecol. 22:245-255.
40. Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K.-H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.
41. Sørensen, J., and B. B. Jørgensen. 1987. Early diagenesis in sediments from Danish coastal waters: microbial activity and Mn-Fe-S geochemistry. Geochim. Cosmochim. Acta 51:1583-1590.
42. Spring, S., R. Amann, W. Ludwig, K.-H. Schleifer, H. van Germerden, and N. Petersen. 1993. Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl. Environ. Microbiol. 59:2397-2403.
43. Teske, A., P. Sigalevich, Y. Cohen, and G. Muyzer. 1996. Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures Appl. Environ. Microbiol. 62:4210-4215.
44. Teske, A., C. Wawer, G. Muzyer, and N. B. Ramsing. 1996. Distribution of sulfate-reducing bacteria in a stratified fjord (Manager 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.
45. Torsvik, V., R. Sørheim, and J. Goksøyr. 1996. Total bacterial diversity in soil and sediment communities - a review. J. Ind. Microbiol. 17:170-178.
46. Vandamme, P., M. Vancanneyt, B. Pot, L. Mels, B. Hoste, D. Dewettinck, L. Vlaes, C. Van den Borre, R. Higgins, J. Hommez, K. Kersters, J.-P. Butzler, and H. Goossens. 1992. Polyphasic taxonomic studies of the emended genus Arcobacter with Arcobacter butzleri comb. nov. and Arcobacter skirrowii sp. nov., an aerotolerant bacterium isolated from veterinary specimens. Int. J. Syst. Bacteriol. 42:344-356.
47. Voordouw, G., S. M. Armstrong, M. F. Reimer, B. Fouts, A. J. Telang, Y. Shen, and D. Gevertz. 1996. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl. Environ. Microbiol. 62:1623-1629.
48. Wellsbury, P., R. A. Herbert, and R. J. Parkes. 1996. Bacterial activity and production in near-surface estuarine and freshwater sediments. FEMS Microbiol. Ecol. 19:203-214.
49. Widdel, F., and F. Bak. 1991. Gram-negative mosophilic sulfate-reducing bacteria, p. 3352-3378. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes. Springer-Verlag, Berlin, Germany.
50. Young-Tae, P., M. Nishimura, and K. Ohwada. 1997. Detection and enumeration of marine sulfate-reducing bacteria using in situ hybridization with 16S rRNA oligonucleotide probes. Fish. Sci. 63:99-104.
51. Zarda, B., D. Hahn, A. Chazinotas, W. Schönhuber, A. Neef, R. I. Amann, and J. Zeyer. 1997. Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch. Microbiol. 168:185-192.