Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 2, 2014, Pages 481-484

  Suarez, Christian ^a   Ratering, Stefan ^a,b   Kramer, Irina ^a   Schnell, Sylvia ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b FRAUNHOFER INSTITUTE FOR SILICATE RESEARCH ISC   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALINE PHOSPHATASE; AMYLOPECTIN; ARYL ACYLAMIDASE; CARBON 14; CASEIN; CITRIC ACID; CYSTINE; DEXTRAN; ERYTHROMYCIN; ESCULIN; ESTERASE; FATTY ACID; GALACTOSE; GLUCONIC ACID; GLUCOSE; KANAMYCIN; LEUCINE; MALIC ACID; MALTOSE; N ACETYLGLUCOSAMINE; PECTIN; PHOSPHATASE; PYRUVIC ACID; RIBOSE; RNA 16S; SODIUM CHLORIDE; SUCROSE; TETRACYCLINE; TRIACYLGLYCEROL LIPASE; UNINDEXED DRUG;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; CELL STRUCTURE; CELLVIBRIO; CELLVIBRIO DIAZOTROPHICUS; GENE SEQUENCE; HORDEUM; HORDEUM SECALINUM; MAXIMUM LIKELIHOOD METHOD; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANTAGO; PLANTAGO WINTERI; PRIORITY JOURNAL; RHIZOSPHERE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CELLVIBRIO; FATTY ACIDS; GERMANY; HORDEUM; MOLECULAR SEQUENCE DATA; NITROGEN FIXATION; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; PLANTAGO; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SALT-TOLERANT PLANTS; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

EID: 84893485915     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.054817-0     Document Type: Article

References (40)

1. Albrecht, S. L. & Okon, Y. (1980). Cultures of Azospirillum. Methods in enzymology, 69, 739-749.
2. Anderson, M. & Habiger, J. (2012). Characterization and identification of productivity-associated rhizobacteria in wheat. Appl Environ Microbiol 78, 4434-4446.
3. Blackall, L. L., Hayward, A. C. & Sly, L. I. (1985). Cellulolytic and dextranolytic Gram-negative bacteria: revival of the genus Cellvibrio. J Bacteriol 59, 81-97.
4. Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248-254.
5. Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75, 4801-4805.
6. DeBoy, R. T., Mongodin, E. F., Fouts, D. E., Tailford, L. E., Khouri, H., Emerson, J. B., Mohamoud, Y., Watkins, K., Henrissat, B. & other authors (2008). Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 190, 5455-5463.
7. Doudoroff, M. & Palleroni, N. J. (1974). Genus I. Pseudomonas Migula 1894. Addendum IV. Bergey's Manual of Determinative Bacteriology, 8th edn, pp. 241-242. Edited by R. E. Buchanan & N. E. Gibbons. Baltimore: Williams & Wilkins.
8. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
9. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
10. Gerhard, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) (1994). Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
11. Gonzalez, J. M. & Saiz-Jimenez, C. (2002). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4, 770-773.
12. 2 fixation: laboratory and field evaluation. Plant Physiol 43, 1185-1207.
13. Heimbrook, M. E., Wang, W. L. L. & Campbell, G. (1989). Staining bacterial flagella easily. J Clin Microbiol 27, 2612-2615.
14. Huber, T., Faulkner, G. & Hugenholtz, P. (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319.
15. Humphry, D. R., Black, G. W. & Cummings, S. P. (2003). Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. Int J Syst Evol Microbiol 53, 393-400.
16. Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989-1005.
17. Kampmann, K., Ratering, S., Kramer, I., Schmidt, M., Zerr, W. & Schnell, S. (2012). Unexpected stability of Bacteroidetes and Firmicutes communities in laboratory biogas reactors fed with different defined substrates. Appl Environ Microbiol 78, 2106-2119.
18. Kasana, R. C., Salwan, R., Dhar, H., Dutt, S. & Gulati, A. (2008). A rapid and easy method for the detection of microbial cellulases on agar plates using Gram's iodine. Curr Microbiol 57, 503-507.
19. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
20. Linkerhägner, K. & Oelze, J. (1997). Nitrogenase activity and regeneration of the cellular ATP pool in Azotobacter vinelandii adapted to different oxygen concentrations. J Bacteriol 179, 1362-1367.
21. Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M. & Schleifer, K. H. (1998). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19, 554-568.
22. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
23. Mergaert, J., Lednická, D., Goris, J., Cnockaert, M. C., De Vos, P. & Swings, J. (2003). Taxonomic study of Cellvibrio strains and description of Cellvibrio ostraviensis sp. nov., Cellvibrio fibrivorans sp. nov. and Cellvibrio gandavensis sp. nov. Int J Syst Evol Microbiol 53, 465-471.
24. Moré, M. I., Herrick, J. B., Silva, M. C., Ghiorse, W. C. & Madsen, E. L. (1994). Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol 60, 1572-1580.
25. Pfennig, N. (1978). Rhodocyclus purpureus gen. nov. and sp. nov., a ring-shaped, vitamin B12-requiring member of the family Rhodospirillaceae. Int J Syst Bacteriol 28, 283-288.
26. Poly, F., Monrozier, L. J. & Bally, R. (2001). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152, 95-103.
27. Pruesse, E., Peplies, J. & Glöckner, F. O. (2012). SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829.
28. Rhee, Y. J., Han, C. R., Kim, W. C., Jun, D. Y., Rhee, I. K. & Kim, Y. H. (2010). Isolation of a novel freshwater agarolytic Cellvibrio sp. KY-YJ-3 and characterization of its extracellular b-agarase. J Microbiol Biotechnol 20, 1378-1385.
29. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
30. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16.
31. 2 conversion ratio in root nodules of Myrica gale L. Plant Physiol 106, 1041-1047.
32. Skerman, V. B. D., McGowan, V. & Sneath, P. H. A. (1980). Approved lists of bacterial names. Int J Syst Bacteriol 30, 225-420.
33. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
34. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
35. Tindall, B. J., Rosselló-Móra, R., Busse, H.-J., Ludwig, W. & Kämpfer, P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60, 249-266.
36. Turner, G. L. & Gibson, A. H. (1980). Measurement of nitrogen fixation by indirect means. In Methods for Evaluating Biological Nitrogen Fixation, pp. 111-139. Edited by F. J. Bergensen. Chichester: Wiley.
37. Voget, S., Steele, H. L. & Streit, W. R. (2006). Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol 126, 26-36.
38. Winogradsky, S. (1929). Études sur la microbiologie du sol. Sur la dégradation de la cellulose dans le sol. Ann Inst Pasteur (Paris) 43, 549-633.
39. Yarza, P., Richter, M., Peplies, J., Euzeby, J., Amann, R., Schleifer, K.-H., Ludwig, W., Glöckner, F. O. & Rosselló-Móra, R. (2008). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31, 241-250.
40. Ziemke, F., Höfle, M. G., Lalucat, J. & Rosselló-Mora, R. (1998). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179-186.