Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats

Applied and Environmental Microbiology

Volumn 71, Issue 4, 2005, Pages 1931-1940

  Schauer, Michael ^a   Hahn, Martin W ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CULTIVATION; FLUORESCENCE; MICROBIOLOGY; OCEAN HABITATS;

BACTERIOPLANKTON; FILAMENTOUS BACTERIA; PHYLOGENIC ANALYSIS;

BACTERIA;

BACTERIUM;

AFRICA; ARTICLE; AUSTRALIA; BACTERIOPLANKTON; BACTERIUM; BACTERIUM CULTURE; BACTERIUM ISOLATION; CHINA; EUROPE; FLUORESCENCE IN SITU HYBRIDIZATION; FRESHWATER ENVIRONMENT; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; HALISCOMENOBACTER HYDROSSIS; LAKE; MORPHOLOGY; MORPHOTYPE; NEW ZEALAND; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGENY; SAPROSPIRACEAE; SPECIES CULTIVATION;

ANIMALS; BACTEROIDETES; DNA PROBES; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; FRESH WATER; GENES, RRNA; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANKTON; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

BACTERIA; CULTIVATION; FLUORESCENCE; HYBRIDIZATION; MICROBIOLOGY;

EID: 17444410849     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.4.1931-1940.2005     Document Type: Article

References (38)

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. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Andersson, A., U. Larsson, and A. Hagström. 1986. Size-selective grazing by a microflagellate on pelagic bacteria. Mar. Ecol. Prog. Ser. 33:51-57.
4. Andreatta, S. 2001. Cytometry of aquatic bacteria: analyses at the community and subgroup level. Ph.D. thesis. University of Innsbruck, Innsbruck, Austria.
5. Bahr, M., J. E. Hobbie, and M. L. Sogin. 1996. Bacterial diversity in an arctic lake: a freshwater SAR11 cluster. Aquat. Microb. Ecol. 11:271-277.
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. Crump, B. C., G. W. Kling, M. Bahr, and J. E. Hobbie. 2003. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69:2253-2268.
8. Glöckner, F. O., E. Zeichikov, 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.
9. 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.
10. Hahn, M. W., P. Stadler, Q. L. Wu, and M. Pöckl. 2004. The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J. Microbiol. Methods 57:379-390.
11. Hiorns, W. D., E. A. Methé, S. A. Nierzwickibauer, and J. P. Zehr. 1997. Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63:2957-2960.
12. Hofer, J. S., and R. Sommaruga. 2001. Seasonal dynamics of viruses in an alpine lake: importance of filamentous forms. Aquat. Microb. Ecol. 26:1-11.
13. Höfle, M. G., H. Haas, and K. Dominik. 1999. Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis. Appl. Environ. Microbiol. 65:3164-3174.
14. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism, vol. 3. Academic Press, New York, N.Y.
15. Keller, M. D., W. K. Bellows, and R. R. L. Guillard. 1988. Microwave treatment for sterilization of phytoplankton culture media. J. Exp. Mar. Biol. Ecol. 117:279-283.
16. Kirchman, D. L. 1993. Statistical analysis of direct counts of microbial abundance, p. 117-119. In P. F. Kemp, B. F. Sherr, E. B. Sherr, and J. J. Cole (ed.), Handbook of methods in aquatic microbial ecology. Lewis Publishers, London, United Kingdom.
17. 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.
18. Kumar, S., K. Tamura, I. B. Jakobson, and M. Nei. 2001. Mega2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
19. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, and N. R. Pace. 1985. Rapid determination of 16S RNA sequences for phylogenetic analysis. Proc. Natl. Acad. Sci. USA 82:6955-6958.
20. Lane, D. J. 1991. 16S/23S rRNA sequencing. Nucleic acid techniques, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Bacterial systematics. John Wiley and Sons, New York, N.Y.
21. Lindström, E. S. 2000. Bacterioplankton community composition in five lakes differing in trophic status and humic content. Microb. Ecol. 40:104-113.
22. 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.
23. 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.
24. 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. C. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, vol. 3.4.4. Kluwer Academic Publishers, Dordrecht, The Netherlands.
25. Pernthaler, J., E. Zöllner, F. Warnecke, and K. Jürgens. 2004. Bloom of filamentous bacteria in a mesotrophic lake: identity and potential controlling mechanism. Appl. Environ. Microbiol. 70:6272-6281.
26. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
27. Schmaljohann, R., U. Pollingher, and T. Hermann. 1987. Natural populations of bacteria in Lake Kinneret: observations with scanning electron and epifluorescence microscopy. Microb. Ecol. 13:1-12.
28. Schmeisser, C., C. Stockigt, C. Raasch, J. Wingender, K. N. Timmis, D. F. Wenderoth, H. C. Flemming, H. Liesegang, R. A. Schmitz, K. E. Jaeger, and W. R. Streit. 2003. Metagenome survey of biofilms in drinking-water networks. Appl. Environ. Microbiol. 69:7298-7309.
29. Sekiguchi, H., M. Watanabe, T. Nakahara, B. Xu, and H. Uchiyama. 2002. Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl. Environ. Microbiol. 68:5142-5150.
30. Semenova, E. A., and K. D. Kuznedelov. 1998. A study of the biodiversity of Baikal picoplankton by comparative analysis of 16S rRNA gene 5′-terminal regions. Mol. Biol. 32:754-760.
31. Urbach, E., K. L. Vergin, L. Young, A. Morse, G. L. Larson, and S. J. Giovannoni. 2001. Unusual bacterioplankton community structure in ultraoligotrophic Crater Lake. Limnol. Oceanogr. 46:557-572.
32. van Veen, W. L., D. van der Kooij, E. C. Geuze, and A. W. van der Vlies. 1973. Investigations of the sheathed bacterium Haliscomenobacter hydrossis gen. n., sp. n., isolated from activated sludge. Antonie Leeuwenhoek 39:207-216.
33. Vrba, J., J. Nedoma, L. Kohout, J. Kopáček, L. Nedbalová, P. Rǎčková, and K. Šimek. 2003. Massive occurrence of heterotrophic filaments in acidified lakes: seasonal dynamics and composition. FEMS Microbiol. Ecol. 46:281-294.
34. Wagner, M., R. Amann, P. Kämpfer, B. Assmus, A. Hartmann, P. Hutzler, N. Springer, and K. H. Schleifer. 1994. Identification and in situ detection of Gram-negative filamentous bacteria in activated sludge. Syst. Appl. Microbiol. 17:405-417.
35. Yannarell, A. C., and E. W. Triplett. 2004. Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales. Appl. Environ. Microbiol. 70:214-223.
36. Yu, Z., and W. W. Mohn. 2001. Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing. Appl. Environ. Microbiol. 67:1565-1574.
37. Zwart, G. J. M., B. C. Crump, M. 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.
38. Zwart, G. J. M., W. D. Hiorns, B. A. Methé, M. P. van Agterveld, R. Huismans, S. C. Nold, J. P. Zehr, and H. J. Laanbroek. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst. Appl. Microbiol. 21:546-556.