Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 4, 2014, Pages 1202-1209

  Suarez, Christian ^a   Ratering, Stefan ^a,b   Geissler Plaum, Rita ^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

ACETYLENE; FATTY ACID; RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; GERMANY; GRAM NEGATIVE BACTERIUM; HORDEUM; HORDEUM SECALINUM; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RHEINHEIMERA HASSIENSIS; RHEINHEIMERA MUENZENBERGENSIS; RHEINHEIMERA NANHAIENSIS; RHEINHEIMERA PACIFICA; RHIZOSPHERE; RNA ANALYSIS; RNA SEQUENCE;

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

EID: 84897948567     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.061200-0     Document Type: Article

References (58)

1. Albrecht, S. L. & Okon, Y. (1980). Cultures of Azospirillum. Methods Enzymol 69, 740-749.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
3. 2-fixing bacterioplankton in the Baltic Sea. Environ Microbiol 9, 152-164.
4. Brettar, I., Christen, R. & Höfle, M. G. (2002). Rheinheimera baltica gen. nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea. Int J Syst Evol Microbiol 52, 1851-1857.
5. Brettar, I., Christen, R. & Höfle, M. G. (2006). Rheinheimera perlucida sp. nov., a marine bacterium of the Gammaproteobacteria isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 56, 2177-2183.
6. 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.
7. Chen, Q., Liu, Z., Peng, Q., Huang, K., He, J., Zhang, L., Li, W. & Chen, Y. (2010a). [Diversity of halophilic and halotolerant bacteria isolated from non-saline soil collected from Xiaoxi National Natural Reserve, Hunan Province]. Wei Sheng Wu Xue Bao 50, 1452-1459 (in Chinese).
8. Chen, W.-M., Lin, C.-Y., Young, C.-C. & Sheu, S.-Y. (2010b). Rheinheimera aquatica sp. nov., an antimicrobial activity producing bacterium isolated from freshwater culture pond. J Microbiol Biotechnol 20, 1386-1392.
9. Chen, W.-M., Yang, S.-H., Young, C.-C. & Sheu, S.-Y. (2013). Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond. Int J Syst Evol Microbiol 63, 1457-1463.
10. Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. & other authors (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37 (Database), D141-D145.
11. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200.
12. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
13. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
14. 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.
15. 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.
16. Halpern, M., Senderovich, Y. & Snir, S. (2007). Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass. Int J Syst Evol Microbiol 57, 1872-1875.
17. 2fixation: laboratory and field evaluation. Plant Physiol 43, 1185-1207.
18. Heimbrook, M. E., Wang, W. L. L. & Campbell, G. (1989). Staining bacterial flagella easily. J Clin Microbiol 27, 2612-2615.
19. Hill, S. & Postgate, J. R. (1969). Failure of putative nitrogen-fixing bacteria to fix nitrogen. J Gen Microbiol 58, 277-285.
20. Huber, T., Faulkner, G. & Hugenholtz, P. (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319.
21. Johnson, J. L. (1994). Similarity analysis of rRNAs. In Methods for General and Molecular Bacteriology, pp. 683-700. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
22. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
23. Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989-1005.
24. Kämpfer, P., Denner, E. B. M., Meyer, S., Moore, E. R. B. & Busse, H. J. (1997). Classification of "Pseudomonas azotocolligans" Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov. Int J Syst Bacteriol 47, 577-583.
25. 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.
26. 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.
27. Kim, J.-S., Dungan, R. S., Kwon, S.-W. & Weon, H.-Y. (2006). The community composition of root-associated bacteria of the tomato plant. World J Microbiol Biotechnol 22, 1267-1273.
28. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
29. Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1-32.
30. 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.
31. Li, H.-J., Zhang, X.-Y., Zhang, Y.-J., Zhou, M.-Y., Gao, Z.-M., Chen, X.-L., Dang, H.-Y. & Zhang, Y.-Z. (2011). Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007. Int J Syst Evol Microbiol 61, 1016-1022.
32. Liu, Y., Jiang, J. T., Xu, C. J., Liu, Y. H., Song, X. F., Li, H. & Liu, Z. P. (2012). Rheinheimera longhuensis sp. nov., isolated from a slightly alkaline lake, and emended description of genus Rheinheimera Brettar et al. 2002. Int J Syst Evol Microbiol 62, 2927-2933.
33. 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.
34. 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.
35. Manter, D. K., Delgado, J. A., Holm, D. G. & Stong, R. A. (2010). Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60, 157-166.
36. Merchant, M. M., Welsh, A. K. & McLean, R. J. C. (2007). Rheinheimera texasensis sp. nov., a halointolerant freshwater oligotroph. Int J Syst Evol Microbiol 57, 2376-2380.
37. 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.
38. Nokhal, T. & Schlegel, H. G. (1983). Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33, 26-37.
39. 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.
40. 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.
41. Prakamhang, J., Minamisawa, K., Teamtaisong, K., Boonkerd, N. & Teaumroong, N. (2009). The communities of endophytic diazotrophic bacteria in cultivated rice (Oryza sativa L.). Appl Soil Ecol 42, 141-149.
42. Pruesse, E., Peplies, J. & Glöckner, F. O. (2012). SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829.
43. Raymond, J., Siefert, J. L., Staples, C. R. & Blankenship, R. E. (2004). The natural history of nitrogen fixation. Mol Biol Evol 21, 541-554.
44. Roesti, D., Ineichen, K., Braissant, O., Redecker, D., Wiemken, A. & Aragno, M. (2005). Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum. Appl Environ Microbiol 71, 6673-6679.
45. Romanenko, L. A., Uchino, M., Falsen, E., Zhukova, N. V., Mikhailov, V. V. & Uchimura, T. (2003). Rheinheimera pacifica sp. nov., a novel halotolerant bacterium isolated from deep sea water of the Pacific. Int J Syst Evol Microbiol 53, 1973-1977.
46. Ryu, S. H., Chung, B. S., Park, M., Lee, S. S., Lee, S.-S. & Jeon, C. O. (2008). Rheinheimera soli sp. nov., a gammaproteobacterium isolated from soil in Korea. Int J Syst Evol Microbiol 58, 2271-2274.
47. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
48. Schwieger, F. & Tebbe, C. C. (1998). A new approach to utilize PCRsingle-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64, 4870-4876.
49. Sierra, G. (1957). A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 23, 15-22.
50. 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.
51. Suarez, C., Ratering, S., Kramer, I. & Schnell, S. (2013). Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio. Int J Syst Evol Microbiol doi:10.1099/ijs.0.054817-0 [Epub ahead of print].
52. 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.
53. Turner, G. L. & Gibson, A. H. (1980). Measurement of nitrogen fixation by indirect means. In Methods for Evaluating Biological Nitrogen Fixation, pp. 111-138. Edited by F. J. Bergensen. Chichester: Wiley.
54. 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.
55. Yoon, J.-H., Bae, S. E., Kang, S. J. & Oh, T.-K. (2007). Rheinheimera aquimaris sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57, 1386-1390.
56. Zehr, J. P., Jenkins, B. D., Short, S. M. & Steward, G. F. (2003). Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5, 539-554.
57. Zhang, X., Sun, L., Qiu, F., McLean, R. J. C., Jiang, R. & Song, W. (2008). Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium. Int J Syst Evol Microbiol 58, 2420-2424.
58. 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. Two novel Rheinheimera species from the rhizosphere http://ijs.sgmjournals.org 1209