Bacterioplankton compositions of lakes and oceans: A first comparison based on fluorescence in situ hybridization

Applied and Environmental Microbiology

Volumn 65, Issue 8, 1999, Pages 3721-3726

  Glöckner, Frank Oliver ^a   Fuchs, Bernhard M ^a   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; FRESH WATER; RIBOSOME RNA; SEA WATER;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; FLAVOBACTERIUM; FLEXIBACTERACEAE; FLUORESCENCE IN SITU HYBRIDIZATION; LAKE; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGENY; SEA; ZOOPLANKTON;

CYTOPHAGA; FLAVOBACTERIUM;

EID: 17644439150     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.8.3721-3726.1999     Document Type: Article

References (69)

1. Amann, R., F. O. Glöckner, and A. Neef. 1997. Modern methods in subsurface microbiology - in situ identification of microorganisms with nucleic acid probes. FEMS Microbiol. Rev. 20:191-200.
2. 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.
3. 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.
4. Bahr, M., J. E. Hobble, and M. L. Sogin. 1996. Bacterial diversity in an arctic lake - a freshwater SAR11 cluster. Aquat. Microb. Ecol. 11:271-277.
5. Baumann, L., P. Baumann, M. Mandel, and R. D. Allen. 1972. Taxonomy of aerobic marine eubacteria. J. Bacteriol. 110:402-429.
6. Benlloch, S., F. Rodriguez Valera, and A. J. Martinez Murcia. 1995. Bacterial diversity in two coastal lagoons deduced from 16S rDNA PCR amplification and partial sequencing. FEMS Microbiol. Ecol. 18:267-279.
7. Bernardet, J. F., P. Segers, M. Vancanneyt, F. Berthe, K. Kersters, and P. Vandamme. 1996. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga quatilis Stohl and Tait 1978. Int. J. Syst. Bacteriol. 46:128-148.
8. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1707-1713.
9. Brosius, J., T. J. 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., B. Rattunde, and K. 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. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
12. 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.
13. DeLong, E. F., K. Y. Wu, B. B. Prezelin, and R. V. M. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697.
14. Fuerst, J. A. 1995. The planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141:1493-1506.
15. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148-149.
16. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59:1294-1302.
17. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
18. 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.
19. Glöckner, F. O., H.-D. Babenzien, and R. Amann. 1998. Phytogeny and identification in situ of Nevskia ramosa. Appl. Environ. Microbiol. 64:1895-1901.
20. Gonzalez, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
21. Gordon, D. A., and S. J. Giovannoni. 1996. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 62:1171-1177.
22. Gosink, J. J., and J. T. Staley. 1995. Biodiversity of gas vacuolate bacteria from Antarctic Sea ice and water. Appl. Environ. Microbiol. 61:3486-3489.
23. Heldal, M., and G. Bratbak. 1991. Production and decay of viruses in aquatic environments. Mar. Ecol. Prog. Ser. 72:205-212.
24. Hicks, R. E., R. I. Amann, and D. A. Stahl. 1992. Dual staining of natural bacterioplankton with 4′,6-diamino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl. Environ. Microbiol. 58:2158-2163.
25. Hiorns, W. D., B. A. Methe, S. A. Nierzwicki-Bauer, and J. P. Zehr. 1997. Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63:2957-2960.
26. Hirsch, P., and G. Rheinheimer. 1968. Biology of budding bacteria. V. Budding bacteria in aquatic habitats: occurrence, enrichment and isolation. Arch. Mikrobiol. 62:289-306.
27. Hovanec, T. A., and E. F. Delong. 1996. Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl. Environ. Microbiol. 62:2888-2896.
28. Kepner, R. L., and J. R. Pratt. 1994. Use of fluorochromes for direct enumaration of total bacteria in environmental samples - past and present. Microbiol. Rev. 58:603-615.
29. Kolter, R., D. A. Siegele, and A. Tormo. 1993. The stationary phase of the bacterial life cycle. Annu. Rev. Microbiol. 47:855-874.
30. MacLeod, R. A. 1965. The question of the existence of specific marine bacteria. Bacteriol. Rev. 29:9-23.
31. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K.-H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142:1097-1106.
32. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.-H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacleria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
33. Marchesi, J. R., T. Sato, A. J. Weightman, T. A. Martin, J. C. Fry, S. J. Hiom, and W. G. Wade. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64:795-799.
34. Mathias C. B., A. K. T. Kirschner, and B. Velimirov. 1995. Seasonal variations of virus abundance and viral control of the bacterial production in a backwater system of the Danube River. Appl. Environ. Microbiol. 61:3734-3740.
35. Methé, B. A., W. D. Hiorns, and J. P. Zehr. 1998. Contrasts between marine and freshwater bacterial community composition - analyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43:368-374.
36. Morita, R. Y. 1992. Low-nutrient environments, p. 617-624. In J. Lederberg (ed.), Encyclopedia of Microbiology, vol. 1. Academic Press, Inc., San Diego, Calif.
37. 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.
38. Murphy, J., and J. P. Riley. 1962. A modified solution method for the determination of phosphate in natural waters. Anal. Chim. Acta 27:31-36.
39. Murray, A. E., C. M. Preston, R. Massana, L. T. Taylor, A. Blakis, K. Wu, and E. F. Delong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:2585-2595.
40. Neef, A. 1997. Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. Ph.D. Thesis. Technische Universität München, Munich, Germany.
41. Neef, A., R. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266.
42. Ouverney, C. C., and J. A. Fuhrman. 1997. Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol. Appl. Environ. Microbiol. 63:2735-2740.
43. Ovreas, L., L. Forney, F. L. Daae, and V. Torsvik. 1997. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63:3367-3373.
44. Painchaud, J., J. C. Therriault, and L. Legendre. 1995. Assessment of salinity-related mortality of freshwater bacteria in the Saint Lawrence estuary. Appl. Environ. Microbiol. 61:205-208.
45. Pernthaler, J., F. O. Glöckner, S. Unterbolzner, A. Alfreider, R. Psenner, and R. Amann. 1998. Seasonal community and population dynamics of pelagic Bacteria and Archaea in a high mountain lake. Appl. Environ. Microbiol. 64:4299-4306.
46. Pernthaler, J., T. Posch, K. Simek, J. Vrba, R. Amann, and R. Psenner. 1997. Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl. Environ. Microbiol. 63:596-601.
47. Pinhassi, J., U. L. Zweifel, and A. Hagstrom. 1997. Dominant marine bacterioplankton species found among colony-forming bacteria. Appl. Environ. Microbiol. 63:3359-3366.
48. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
49. Rappé, M. S., M. T. Suzuki, K. L. Vergin, and S. J. Giovannoni. 1998. Phylogenetic diversity of ultraplankton plastid small-subunit rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States. Appl. Environ. Microbiol. 64:294-303.
50. Rath, J., K. Y. Wu, G. J. Herndl, and E. F. Delong. 1998. High phylogenetic diversity in a marine-snow-associated bacterial assemblage. Aquat. Microb. Ecol. 14:261-269.
51. Rheinheimer, G. 1996. Meereskunde der Ostsee, 2nd ed. Springer-Verlag, Berlin, Germany.
52. Roszak, D. B., and R. R. Colwell. 1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51:365-379.
53. Schlesner, H. 1994. The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media. Syst. Appl. Microbiol. 17:135-145.
54. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
55. Schönhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.
56. Shewan, J. M., and T. A. McMeekin. 1983. Taxonomy (and ecology) of Flavobacterium and related genera. Annu. Rev. Microbiol. 37:233-252.
57. 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.
58. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, United Kingdom.
59. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
60. Suzuki, M. T., M. S. Rappe, Z. W. Haimberger, H. Winfield, N. Adair, J. Strobel, and S. J. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63:983-989.
61. Vollenweider, R. A. 1968. Scientific fundamentals of the eutrophication of lakes and flowing waters, with particular reference to nitrogen and phosphorus as factors in eutrophication. Organisation for Economic Cooperation and Development, Paris, France.
62. Voytek, M. A., and B. B. Ward. 1995. Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl. Environ. Microbiol. 61:1444-1450.
63. Wagner, M., R. Amann, H. Lemmer, and K.-H. Schleifer. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.
64. Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescent in situ-hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.
65. Weinbauer, M. G., and C. A. Suttle. 1997. Comparison of epifluorescence and transmission electron microscopy for counting viruses in natural marine waters. Aquat. Microb. Ecol. 13:225-232.
66. Weiss, P., B. Schweitzer, R. Amann, and M. Simon. 1996. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl. Environ. Microbiol. 62:1998-2005.
67. Wright, T. D., K. L. Vergin, P. W. Boyd, and S. J. Giovannoni. 1997. A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. Environ. Miciobiol. 63:1441-1448.
68. Zavarzin, G. A., E. Stackebrandt, and R. G. Murray. 1991. A correlation of phylogenetic diversity in the Proteobacteria with the influences of ecological forces. Can. J. Microbiol. 37:1-6.
69. Zobell, C. E., and H. C. Upham. 1944. A list of marine bacteria including descriptions of sixty new species. Bull. Scripps Inst. Oceanogr. 5:239-292.