High phylogenetic diversity of Flavobacterium spp. isolated from a hardwater creek, Harz Mountains, Germany

Organisms Diversity and Evolution

Volumn 7, Issue 2, 2007, Pages 145-154

  Brambilla, Evelyne ^a   Päuker, Orsola ^a   Cousin, Sylvie ^a   Steiner, Ulrike ^a   Reimer, Andreas ^b   Stackebrandt, Erko ^a  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

16S rRNA gene sequence similarities; Flavobacterium; Freshwater microbial diversity; Phylogeny

Indexed keywords

BACTERIUM; GENETIC ANALYSIS; PHYLOGENY; SPECIES DIVERSITY; TAXONOMY;

CENTRAL EUROPE; EURASIA; EUROPE; GERMANY; HARZ MOUNTAINS; LOWER SAXONY; WESTERHOFER BACH;

BACTEROIDETES; EPILITHONIMONAS TENAX; FLAVOBACTERIACEAE; FLAVOBACTERIUM; PERSICIVIRGA XYLANIDELENS; PROTEOBACTERIA;

EID: 33847224429     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1016/j.ode.2006.03.003     Document Type: Article

References (34)

1. Amann R.I., Ludwig W., and Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 (1995) 143-169
2. Arp G., Wedemeyer N., and Reitner J. Fluvial tufa formation in a hard-water creek, Deinschwanger Bach, Franconian Alb, Germany). Facies 44 (2001) 1-22
3. Bernadet, J.-F., Bowman, J.P., 2005. The genus Flavobacterium. In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (Eds.), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd ed., release 3.20. Springer, New York 〈http://link.springer-ny.com/link/service/books/10125/〉.
4. Brambilla E., Hippe H., Hagelstein A., Tindall B.J., and Stackebrandt E. 16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antartica. Extremophiles 5 (2001) 22-33
5. Burns B.P., Seifert A., Goh F., Pomati F., Jungblut A.-D., Serhat A., and Neilan B.A. Genetic potential for secondary metabolite production in stromatolite communities. FEMS Microbiol. Lett. 243 (2005) 293-301
6. Crump B.C., Armbrust E.V., and Baross J.A. 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 (1999) 3192-3204
7. DSMZ Catalogue of Strains. Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (2001), Braunschweig, Germany
8. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 30 (1985) 783-791
9. Felsenstein J. PHYLIP Phylogenetic Inference Package, version 3.5.1 (1993), Department of Genetics, University of Washington, Seattle, USA
10. Fenselau C., and Demirev P.A. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20 (2001) 157-171
11. Freytet P., and Plet A. Modern freshwater microbial carbonates: the Porphyridium stromatolites (tufa-travertine) of south-eastern Burgundy (Paris basin, France). Facies 34 (1996) 219-238
12. Fritsch F.E. Porphyridium incrustatum (Naeg.) Gom., an important member of the lime incrusted communities of flowing waters. Biol. Jahrb. 17 (1950) 27-39
13. Gerdes G., Klenke T., and Noffke N. Microbial signatures in peritidal siliciclastic sediments: a catalogue. Sedimentology 47 (2000) 279-308
14. Gosink J.J., Woese C.R., and Staley J.T. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int. J. Syst. Bacteriol. 48 (1998) 223-235
15. Herman J.S., and Lorah M.M. Calcite precipitation rates in the field: measurement and prediction for a travertine-depositing stream. Geochim. Cosmochim. Acta 52 (1988) 2347-2355
16. Irion G., and Müller G. Mineralogy, petrology and chemical composition of some calcareous tufa from the Schwäbische Alb, Germany. In: Müller G., and Friedman G.M. (Eds). Recent Developments in Carbon Sedimentology in Central Europe (1968), Springer, Heidelberg 157-171
17. Karpouzas D.G., Fotopoulou A., Menkissoglu-Spiroudi U., and Singh B.K. Non-specific biodegradation of the organophosphorus pesticides, cadusafos and ethoprophos, by two bacterial isolates. FEMS Microbiol. Ecol. 53 (2005) 369-378
18. 3 precipitation. Prep. Biochem. Biotechnol. 32 (2002) 51-63
19. Kawaguchi T., Sayegh H.A., and Decho A.W. Development of an indirect competitive enzyme linked immunosorbent assay to detect extracellular polymeric substances (EPS) secreted by the marine stromatolite-forming cyanobacteria, Schizothrix sp. J. Immunoassay Immunochem. 24 (2003) 29-39
20. Lee C.C., Smith M., Kibblewhite-Accinelli R.E., Williams T.G., Wagschal K., Robertson G.H., and Wong D.W.S. Isolation and characterization of a cold-active xylanase enzyme from Flavobacterium sp. Curr. Microbiol. 52 (2006) 112-116
21. Maidak B.L., Cole J.R., Lilburn T.G., Parker Jr. C.T., Saxman P.R., Farris R.J., Garrity G.M., Olsen G.J., Schmidt T.M., and Tiedje J.M. The RDP-II Ribosomal Database Project. Nucl. Acids Res. 29 (2001) 173-174
22. Miller, L., Berger, T., 1984. Bacterial identification by gas chromatography and whole cell fatty acids. Gas Chromatography Application Note 228-41. Hewlett-Packard Co., Palo Alto, CA.
23. Neilan B.A., Burns B.P., Relman D.A., and Lowe D.R. Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locations. Astrobiology 2 (2002) 271-280
24. O'Sullivan L.A., Rinna J., Humphreys G., Weightman A.J., and Fry J.C. Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 56 (2006) 169-180
25. Oikawa T., Yamamoto N., Shimoke K., Uesato S., Ikeuchi T., and Fujioka T. Purification, characterization, and overexpression of psychrophilic and thermolabile malate dehydrogenase of a novel Antarctic psychrotolerant, Flavobacterium frigidimaris KUC-1. Biosci. Biotechnol. Biochem. 69 (2005) 2146-2154
26. Papineau D., Walker J.J., Mojzsis S.J., and Pace N.R. Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl. Environ. Microbiol. 71 (2005) 4822-4832
27. Pentecost A., and Riding R. Calcification in cyanobacteria. In: Leadbeater B.S.C., and Riding R. (Eds). Biomineralization of Lower Plants and Animals (1986), Clarendon, Oxford 73-90
28. Pentecost A. Blue-green algae and freshwater carbonate deposits. Proc. R. Soc. London B 200 (1978) 43-61
29. Rainey F.A., Ward-Rainey N., Kroppenstedt R.M., and Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam nov. Int. J. Syst. Bacteriol. 46 (1996) 1088-1092
30. Riding R. Classification of microbial carbonates. In: Riding R. (Ed). Calcareous Algae and Stromatolites (1991), Springer, Berlin 21-51
31. Ryzhof V., and Fenselau C. Characterization of the protein subset desorbed by MALDI from whole bacterial cells. Anal. Chem. 73 (2001) 746-750
32. Steppe T.F., Pinckney J.L., Dyble J., and Paerl H.W. Diazotrophy in modern marine Bahamina stromatolites. Microb. Ecol. 41 (2001) 36-44
33. Tindall B.J., Brambilla E., Steffen M., Neumann R., Pukall R., Kroppenstedt R.M., and Stackebrandt E. Cultivatable microbial diversity: gnawing at the Gordian knot. Environ. Microbiol. 2 (2000) 310-318
34. 3 precipitation. Earth Planet. Sci. Lett. 42 (1979) 267-276