Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of β-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir

Applied and Environmental Microbiology

Volumn 71, Issue 5, 2005, Pages 2381-2390

  Šimek, Karel ^a,b   Horňák, Karel ^a,b   Jezbera, Jan ^a,b   Mašín, Michal ^a   Nedoma, Jiří ^a   Gasol, Josep M ^c   Schauer, Michael ^d  

^a INSTITUTE OF HYDROBIOLOGY   (Czech Republic)

^b UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^c INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^d ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROPHORESIS; GELS; MICROBIOLOGY; NUCLEIC ACIDS; PHOSPHORUS; PLANTS (BOTANY); WATER;

BACTERIAL DYNAMICS AND COMMUNITY COMPOSITION (BCC); BOTTOM-UP MANIPULATIONS; NANOFLAGELLATES; PROTISTAN GRAZING;

BACTERIA;

NUCLEIC ACID;

COMMUNITY COMPOSITION; COMMUNITY DYNAMICS; MICROBIAL COMMUNITY; NUTRIENT AVAILABILITY; RESERVOIR;

ACTINOBACTERIA; ARTICLE; BACTERIOPLANKTON; BACTERIVORY; BETAPROTEOBACTERIA; FLUORESCENCE IN SITU HYBRIDIZATION; FRACTIONATION; FRESHWATER ENVIRONMENT; GEL ELECTROPHORESIS; GENE CLUSTER; MOLECULAR DYNAMICS; NONHUMAN; PHYLOGENY; RESERVOIR;

ANIMALS; BETAPROTEOBACTERIA; BIOMASS; ECOSYSTEM; FOOD CHAIN; FRESH WATER; MASTIGOPHORA; NUCLEIC ACIDS; PHOSPHORUS; PLANKTON;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; PROTISTA;

EID: 18444363645     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.5.2381-2390.2005     Document Type: Article

References (52)

1. Alfreider, A., J. Pernthaler, R. Amann, B. Sattler, F.-O. Glöckner, A. Ville, and R. Psenner. 1996. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake using in situ hybridization. Appl. Environ. Microbiol. 62:2138-2144.
2. Beardsley, C., J. Pernthaler, W. Wosniok, and R. Amann. 2003. Are readily culturable bacteria in coastal North Sea waters suppressed by selective grazing mortality? Appl. Environ. Microbiol. 69:2624-2630.
3. Bouvier, T. C., and P. A. del Giorgio. 2002. Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol. Oceanogr. 47:453-470.
4. Burkert, U., F. Warnecke, D. Babenzien, E. Zwirnmann, and J. Pernthaler. 2003. Members of a readily enriched β-proteobacterial clade are common in surface waters of a humic lake. Appl. Environ. Microbiol. 69:6550-6559.
5. Cottrell, M. T., and D. L. Kirchman. 2004. Single-cell analysis of bacterial growth, cell size, and community structure in the Delaware estuary. Aquat. Microb. Ecol. 34:39-149.
6. Crump, B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65:3192-3204.
7. del Giorgio, P. A., and T. C. Bouvier. 2002. Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient. Limnol. Oceanogr. 47:471-486.
8. del Giorgio, P. A., J. M. Gasol, D. Vaqué, P. Mura, S. Agostí, and C. M. Duarte. 1996. Bacterioplankton community structure: protists control net production and the proportion of active bacteria in a coastal marine community. Limnol. Oceanogr. 41:1169-1179.
9. Eilers, H., J. Pernthaler, and R. Amann. 2000. Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl. Environ. Microbiol. 66:4634-4640.
10. Fuchs, B. M., M. V. Zubkov, K. Sahm, P. H. Burkill, and R. Amann. 2000. Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Environ. Microbiol. 2:191-201.
11. Gasol, J. M., M. Comerma, J.-C. Garcia, J. Armengol, E. O. Casamayor, P. Kojecká, and K. Šimek. 2002. A transplant experiment to identify the factors controlling bacterial abundance, activity, production and community composition in a eutrophic canyon-shaped reservoir. Limnol. Oceanogr. 47:62-77.
12. Gasol, J. M., and P. A. del Giorgio. 2000. Using flow cytometry for counting natural plaktonic bacteria and understanding the structure of planktonic bacterial communities. Sci. Mar. 64:197-224.
13. Gasol, J. M., U. L. Zweifel, F. Peters, J. A. Fuhrman, and A. Hagstrom. 1999. Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria. Appl. Environ. Microbiol. 65:475-4483.
14. Glöckner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization Appl. Environ. Microbiol. 65:3721-3726.
15. Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.
16. Hahn, M. W. 2003. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl. Environ. Microbiol. 69:5248-5254.
17. Hahn, M. W., and M. G. Höfle. 2001. Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol. Ecol. 35:113-121.
18. Hahn, M. W., H. Lünsdorf, Q. Wu, M. Schauer, M. G. Höfle, J. Boenigk, and P. Stadler. 2003. Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl. Environ. Microbiol. 69:1442-1451.
19. Jezbera, J., J. Nedoma, and K. Šimek. 2003. Longitudinal changes in protistan bacterivory and bacterial production in two differently loaded canyon-shaped reservoirs. Hydrobiologia 504:115-130.
20. Jürgens, K. 1994. Impact of Daphnia on planktonic microbial food webs - a review. Mar. Microb. Food Webs 8:295-324.
21. Jürgens, K., J. Pernthaler, S. Schalla, and R. Amann. 1999. Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl. Environ. Microbiol. 65:1241-1250.
22. Kirchman, D. L., L. Yu, B. M. Fuchs, and R. Amann. 2001. Structure of bacterial communities in aquatic systems as revealed by filter PCR. Aquat. Microb. Ecol. 26:13-22.
23. Kopáček, J., and J. Hejzlar. 1993. Semi-micro determination of total phosphorus in fresh waters with perchloric acid digestion. Int. J. Environ. Anal. Chem. 53:173-183.
24. Lebaron, P., P. Servais, H. Agogue, C. Courties, and F. Joux. 2001. Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl. Environ. Microbiol. 67:1775-1782.
25. Lebaron, P., P. Servais, A.-C. Baudoux, M. Bourrain, C. Courties, and N. Parthuisot. 2002. Variations of bacterial-specific activity with cell size and nucleic acid content assessed by flow cytometry. Appl. Environ. Microbiol. 68:131-140.
26. Mašín, M., K. Šimek, J. Jezbera, J. Nedoma, V. Straškrabová, and J. Hejzlar. 2003. Changes in bacterial community composition and microbial activities along the longitudinal axis of two differently loaded canyon-shaped reservoirs. Hydrobiologia 504:99-113.
27. Muyzer, G., T. Brinkhoff, U. Nübel, C. Santegoeds, H. Schäfer, and C. Wawer. 1997. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-27. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, 2nd ed., vol. 3. Kluwer Academic Publishers, Dordrecht, The Netherlands.
28. Nedoma, J., P. Porcalová, J. Komárková, and V. Vyhnálek. 1993. Phosphorus deficiency diagnostics in the eutrophic Římov reservoir. Water Sci. Technol. 28:75-84.
29. Norland, S. 1993. The relationship between biomass and volume of bacteria, p. 303-308. In P. Kemp, B. F. Sherr, E. B. Sherr, and J. Cole (ed.), Handbook of methods in aquatic microbial ecology. Lewis, Boca Raton, Fla.
30. Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.
31. Pernthaler, J., T. Posch, K. Šimek, J. Vrba, U. Nübel, F.-O. Glöckner, R. Psenner, and R. Amann. 2001. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in a mixed continuous culture. Appl. Environ. Microbiol. 67:2145-2155.
32. Posch, T., J. Pernthaler, A. Alfreider, and R. Psenner. 1997. Cell-specific respiratory activity of aquatic bacteria studied with the tetrazolium reduction method, Cyto-Clear slides, and image analysis. Appl. Environ. Microbiol. 63:867-873.
33. Posch, T., K. Šimek, J. Vrba, S. Pernthaler, J. Nedoma, B. Sattler, B. Sonntag, and R. Psenner. 1999. Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquat. Microb. Ecol. 18:235-246.
34. Riemann, B., and M. Søndergaard. 1986. Carbon dynamics in eutrophic, temperate lakes. Elsevier Science Publishers, Amsterdam, The Netherlands.
35. Riemann, L., G. F. Steward, and F. Azam. 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66:578-587.
36. Rigler, F. H. 1966. Radiobiological analysis of inorganic phosphorus in lake water. Vehr. Int. Verein. Limnol. 16:465-470.
37. Schäfer, H., L. Bernard, C. Courties, P. Lebaron, P. Servais, R. Pukall, E. Stackebrandt, M. Troussellier, T. Guindulain, J. Vives-Rego, and G. Muyzer. 2001. Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol. Ecol. 34:243-253.
38. Schauer, M., V. Balagué, C. Pedrós-Alió, and R. Massana. 2003. Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system. Aquat. Microb. Ecol. 31:163-174.
39. Sekar, R., A. Pernthaler, J. Pernthaler, F. Warnecke, T. Posch, and R. Amann. 2003. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2928-2935.
40. Servais, P., C. Courties, P. Lebaron, and M. Trousellier. 1999. Coupling bacterial activity measurements with cell sorting by flow cytometry. Microb. Ecol. 38:180-189.
41. Sherr, B. F., E. B. Sherr, and J. McDaniel. 1992. Effect of protistan grazing on the frequency of dividing cells in bacterioplankton assemblage. Appl. Environ. Microbiol. 58:2381-2385.
42. Sherr, E. B., and B. F. Sherr. 1993. Protistan grazing rates via uptake of fluorescently labelled prey, p. 695-701. In P. Kemp, B. F. Sherr, E. B. Sherr, and J. Cole (ed.), Handbook of methods in aquatic microbial ecology. Lewis, Boca Raton, Fla.
43. Šimek, K., K. Horňák, M. Mašín, U. Christaki, J. Nedoma, M. G. Weinbauer, and J. R. Dolan. 2003. Comparing the effects of resource enrichment and grazing on a bacterioplankton community of a meso-eutrophic reservoir. Aquat. Microb. Ecol. 31:123-135.
44. Šimek, K., P. Kojecka, J. Nedoma, P. Hartman, J. Vrba, and D. R. Dolan. 1999. Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnol. Oceanogr. 44:1634-1644.
45. Šimek, K., J. Nedoma, J. Pernthaler, T. Posch, and J. R. Dolan. 2002. Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition. Antonie Leeuwenhoek 81:453-463.
46. Šimek, K., J. Pernthaler, M. G. Weinbauer, K. Horňá k, J. R. Dolan, J. Nedoma, M. Mašin, and R. Amann. 2001. Changes in bacterial community composition, dynamics, and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl. Environ. Microbiol. 67:2723-2733.
47. Vaqué, D., E. O. Casamayor, and J. M. Gasol. 2001. Dynamics of whole community bacterial production and grazing losses in seawater incubations as related to the changes in the proportions of bacteria with different DNA content. Aquat. Microb. Ecol. 25:163-177.
48. Warnecke, F., R. Amann, and J. Pernthaler. 2004. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ. Microbiol. 6:242-253.
49. Weinbauer, M. G., K. Šimek, U. Christaki, and J. Nedoma. 2003. Comparing the effects of resource enrichment and grazing on viral production in a meso-eutrophic reservoir. Aquat. Microb. Ecol. 31:137-144.
50. Zubkov, M. V., B. M. Fuchs, P. H. Burkill, and R. Amann. 2001. Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl. Environ. Microbiol. 67:5210-5218.
51. Zwart, G., B. C. Crump, M. P. Kamst-van Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155.
52. Zwart, G., E. J. van Hannen, M. P. Kamst-van Agterveld, K. Van der Gucht, E. S. Lindstrom, J. Van Wichelen, T. Lauridsen, B. C. Crump, S. K. Han, and S. Declerck. 2003. Rapid screening for freshwater bacterial groups by using reverse line blot hybridization. Appl. Environ. Microbiol. 69:5875-5883.