Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

Environmental Microbiology

Volumn 6, Issue 12, 2004, Pages 1228-1243

  Eiler, Alexander ^a   Bertilsson, Stefan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; FRESH WATER; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CYANOBACTERIUM; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PLANKTON; RNA GENE; SWEDEN;

BACTERIA; BIODIVERSITY; CYANOBACTERIA; DNA, BACTERIAL; DNA, RIBOSOMAL; FRESH WATER; GENES, RRNA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANKTON; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SWEDEN; WATER MICROBIOLOGY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; PLANCTOMYCETES; PROKARYOTA; PROTEOBACTERIA; VERRUCOMICROBIA;

EID: 10044278979     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00657.x     Document Type: Article

References (63)

1. Bertilsson, S., and Jones, J. (2003) Supply of dissolved organic matter to aquatic ecosystems: Autochthonous sources. In Aquatic Ecosystems: Interactivity of Dissolved Organic Matter. Findlay, S.E.G., and Sinsabaugh, R.L. (eds). Amsterdam, the Netherlands: Academic Press, pp. 3-24.
2. Bosshard, P.P., Santini, Y., Grüter, D., Stettler, R., and Bachofen, R. (1999) Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS Microbiol Ecol 31: 173-182.
3. Brunberg, A.K., and Boström, B. (1992) Coupling between benthic biomass of Microcystis and phosphorus release from the sediments of a highly eutrophic lake. Hydrobiologia 235/236: 375-385.
4. Burkert, U., Warnecke, F., Babenzien, D., Zwirnmann, E., and Pernthaler, J. (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. Chao, A. (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
6. Cole, J.J., Likens, G.E., and Strayer, D.L. (1982) Photosynthetically produced dissolved organic carbon: an important carbon source for planktonic bacteria. Limnol Oceanogr 27: 1080-1090.
7. Cottrell, M.T., and Kirchman, D.L. (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66: 5116-5122.
8. Crump, B.C., Kling, G.W., Bahr, M., and Hobbie, J.E. (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 69: 2253-2268.
9. Dean, W.E., and Gorham, E. (1998) Magnitude and significance of carbon burial in lakes, reservoirs and peatlands. Geology 26: 535-538.
10. Egert, M., and Friedrich, M.W. (2003) Formation of pseudoterminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69: 2555-2562.
11. Eiler, A., Langenheder, S., Bertilsson, S., and Tranvik, L.J. (2003) Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations. Appl Environ Microbiol 69: 3701-3709.
12. Eilers, H., Pernthaler, J., Glöckner, F.O., and Amann, R. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66: 3044-3051.
13. Engström-Öst, J., Koski, M., Schmidt, K., Viitasalo, M., Jónasdóttir, S.H., Kokkonen, M., Repka, S., and Sivonen, K. (2002) Effects of toxic cyanobacteria on a plankton assemblage: community development during decay of Nodularia spumigena. Mar Ecol Progr Series 232: 1-14.
14. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
15. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
16. Glöckner, F.O., Fuchs, B., and Amann, R. (1999) Bacterioplankton composition of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65: 3721-3726.
17. Glöckner, F.O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A., and Amann, R. (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.
18. Gorham, P.R., and Carmichael, W.W. (1988) Hazards of freshwater blue-green algae (cyanobacteria). In Algae and Human Affairs. Lembe, C.A., and Waaland, J.R. (eds). Cambridge, UK: University Press, pp. 403-431.
19. 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.
20. Hahn, M.W., Lünsdorf, H., Wu, Q., Schauer, M., Höfle, M.G., Boenigk, J., and Stadler, P. (2003) Isolation of novel ultra-microbacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl Environ Microbiol 69: 1442-1451.
21. Hill, T.C.J., Walsh, K.A., Harris, J.A., and Moffet, B. (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43: 1-11.
22. Hiorns, W.D., Methe, B.A., Nierzwickibauer, S.A., and Zehr, J.P. (1997) Bacterial diversity in Adirondack Mountain lakes as revealed by 16S rRNA gene sequences. Appl Environ Microbiol 63: 2957-2960.
23. Humayoun, S.B., Bano, N., and Hollibaugh, J.T. (2003) Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Appl Environ Microbiol 69: 1030-1042.
24. Jespersen, A.-M., and Christoffersen, K. (1987) Measurement of chlorophyll-a from phytoplankton using ethanol as extraction solvent. Arch Hydrobiol 109: 445-454.
25. Karlsson Elfgren, I. (2003) Studies on the Life Cycles of Akinete Forming Cyanobacteria. Acta Universitatis Upsaliensis. Comprehensive summaries of Uppsala Dissertations from the Faculty of Science and Technology, No. 856. Uppsala, Sweden.
26. Kelly, K.M., and Chistoserdov, A.Y. (2001) Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol Ecol 35: 85-95.
27. Kirchman, D.L. (2001) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39: 91-100.
28. Kisand, V., Cuadros, R., and Wikner, J. (2001) Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern Baltic Sea. Appl Environ Microbiol 68: 379-388.
29. Konopka, A., Bercot, T., and Nakatsu, C. (1999) Bacterioplankton community diversity in a series of thermally stratified lakes. Microb Ecol 38: 126-135.
30. Kuhner, M.K., and Felsenstein, J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11: 459-468 (Erratum 12: 525; 1995).
31. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester: Wiley and Sons, pp. 115-175.
32. Lane, D.L., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82: 6955-6959.
33. Lindström, E.S. (2000) Bacterioplankton community composition in five lakes differing in trophic status and humic content. Microb Ecol 40: 104-113.
34. Lindström, E.S., and Leskinen, E. (2002) Do neighbouring lakes share common taxa in bacterioplankton? Comparison of 16S rRNA fingerprints and sequences from three geographic regions. Microb Ecol 44: 1-9.
35. Mur, L.R., Skulberg, O.M., and Utkilen, H. (1999) Cyanobacteria in the environment. In Toxic Cyanobacteria in Water: a Guide to Their Public Health Consequences, Monitoring and Management. Chorus, I., and Bartram, J. (eds). London: E & FN Spon, pp. 15-40.
36. Neef, A., Amann, R., Schlesner, H., and Schleiker, K.-H. (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-target probes. Microbiology 144: 3257-3266.
37. Oliver, R.L., and Ganf, G.G. (2000) Freshwater blooms. In The Ecology of Cyanobacteria; Their Diversity in Time and Space. Whitton, B.A., and Potts, M. (eds). Dordrecht, the Netherlands: Kluwer, pp. 150-194.
38. Østensvik, Ø., Skulberg, O.M., Underdal, B., and Hormazabal, V. (1998) Antibacterial properties of extracts from selected planktonic freshwater Cyanobacteria - a comparative study of bacterial bioassays. J Appl Microbiol 84: 1117-1124.
39. Pernthaler, J., Posch, T., Simek, K., Vrba, J., Pernthaler, A., Glöckner, F.O., et al. (2001) Predator-specific enrichment of Actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol 65: 25-35.
40. Polz, M.F., and Cavanaugh, C.M. (1998) Bias in product-to-template ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
41. Porter, K.G., and Feig, Y.S. (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 843-948.
42. Rashidan, K.K., and Bird, D.F. (2001) Role of predatory bacteria in the termination of a cyanobacterial bloom. Microb Ecol 41: 97-105.
43. Riemann, L., and Winding, A. (2001) Community dynamics of free-living and particle-associated bacterial assemblages during a freshwater phytoplankton bloom. Microb Ecol 42: 274-285.
44. Ritz, K., Griffiths, B.S., Torsvik, V.L., and Hendriksen, N.B. (1997) Analysis of soil and bacterioplankton community DNA by melting profiles and reassociation kinetics. FEMS Microbiol Lett 149: 151-156.
45. Rossello-Mora, R., and Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 36-79.
46. Sambrook, J., and Russel, D.W. (2001) Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press.
47. Sekar, R., Pernthaler, A., Pernthaler, J., Warnecke, F., Posch, T., and Amann, R. (2003) An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridisation. Appl Environ Microbiol 69: 2928-2935.
48. Sekiguchi, H., Koshikawa, H., Hiroki, M., Murakami, S., Xu, K., Watanabe, M., et al. (2002) Bacterial distribution and phylogenetic diversity in the Changjiang estuary before the construction of the Three Gorges Dam. Microb Ecol 43: 82-91.
49. Selje, N., and Simon, M. (2003) Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany. Aquat Microb Ecol 30: 221-237.
50. Simon, M., and Azam, F. (1989) Protein content and protein synthesis rate of planktonic marine bacteria. Mar Ecol Progr Series 51: 201-213.
51. 3H-leucine. Mar Microb Food Webs 6: 107-114.
52. Søndergaard, M., and Middelboe, M. (1995) A cross-system analysis of labile dissolved organic carbon. Mar Ecol Progr Series 118: 283-294.
53. Søndergaard, M., Borch, N.H., and Riemann, B. (2000) Dynamics of biodegradable DOC produced by freshwater plankton communities. Aquat Microb Ecol 23: 73-83.
54. Staley, J.T., Fuerst, J.A., Giovannoni, S., and Schlesner, H. (1992) The order Planctomycetales and the genera Planctomyces, Pirellula, Gemmata, and Isosphaera. In The Prokaryotes, 2nd edn, Vol. IV. Balows, A., Truper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds). New York, USA: Springer, pp. 3710-3731.
55. Strunk, O., and Ludwig, W. (1996) ARB: A Software Environment for Sequence Data, 2.1.1. Munich: Department of Microbiology, Technical University of Munich.
56. Trusova, M.Yu and Gladyshev, M.I. (2002) Phylogentic diversity of winter bacterioplankton of eutrophic Sibirean reservoirs as revealed by 16S rRNA gene sequences. Microb Ecol 44: 252-259.
57. Urbach, E., Vergin, K.L., Young, L., Morse, A., Larson, G.L., and Giovannoni, S.J. (2001) Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 46: 557-572.
58. Van der Gucht, K., Sabbe, K., De Meester, L., Vloemans, N., Zwart, G., Gillis, M., and Vyverman, W. (2001) Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes. Environ Microbiol 3: 680-690.
59. Van Hannen, E.J., Zwart, G., Van Agterveld, M.P., Gons, H.J., Ebert, J., and Laanbroek, H.J. (1999) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ Microbiol 65: 795-801.
60. Vergin, K.L., Urbach, E., Stein, J.L., DeLong, E.F., Lanoil, B.D., and Giovannoni, S.J. (1998) Screening a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol 64: 3075-3078.
61. Warnecke, F., Amann, R., and Pernthaler, J. (2004) Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ Microbiol 6: 242-253.
62. Zwart, G., Crump, B.C., Kamst-van Agterveld, M., Hagen, F., and Han, S.-K. (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28: 141-155.
63. Zwart, G., van Hannen, E.J., Kamst-van Agterfeld, M.P., Van der Gucht, K., Lindström, E.S., Van Wichelen, J., et al. (2003) Rapid screening of freshwater bacterial groups by using reverse line blot hybridization. Appl Environ Microbiol 69: 5875-5883.