1887

Abstract

The genus of the mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. The plant-associated bacterial isolates N3, N5 and N9 were derived from surface-sterilized wheat roots. After phylogenetic analysis of 16S rRNA gene sequence data the isolates could be allocated to the genus , and 99.9 % similarity to the sequence of P6-12 was found. A set of 16S rRNA gene-targeted oligonucleotide probes was developed for the identification of the three novel isolates and (Hhilu446), and for the specific detection of several other species described recently. For higher phylogenetic resolution, the 23S rRNA gene sequences of all members of the genus was sequenced and used to construct a phylogenetic tree. Isolates N3, N5 and N9 formed a group that was distinct from all other species. In addition, isolate N3 and P6-12 exhibited a DNA–DNA hybridization value of only 25 %. The value for DNA–DNA hybridization between N3 and other members of the genus was between 14 and 32 %; DNA–DNA hybridization between strain N3 and isolates N5 and N9 produced values above 95 %. This places the three isolates as representatives of a novel species within the genus . A Biolog GN2 assay supported this conclusion. The major fatty acids were C 7, C and C 7, and the DNA G+C content ranged from 60.9 to 61.5 mol%. Therefore these three isolates should be classified within a novel species, for which the name sp. nov. is proposed. The type strain is N3 (=DSM 17495=LMG 23131).

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2006-06-01
2019-09-21
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References

  1. Amann, R. I., Krumholz, L. & Stahl, D. A. ( 1990; ). Fluorescent-oligonucleotide probing of whole cells for determinative and environmental studies in microbiology. J Bacteriol 172, 762–770.
    [Google Scholar]
  2. Amann, R. I., Zarda, B., Stahl, D. A. & Schleifer, K. H. ( 1992; ). Identification of individual prokaryotic cells by using enzyme-labeled, rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 58, 3007–3011.
    [Google Scholar]
  3. Amoozegar, M. A., Malekzadeh, F., Malik, K. A., Schumann, P. & Sproer, C. ( 2003; ). Halobacillus karajensis sp. nov., a novel moderate halophile. Int J Syst Evol Microbiol 53, 1059–1063.[CrossRef]
    [Google Scholar]
  4. Bae, H. S., Lee, J. M., Kim, Y. B. & Lee, S. T. ( 1996; ). Biodegradation of the mixtures of 4-chlorophenol and phenol by Comamonas testosteroni CPW301. Biodegradation 7, 463–469.
    [Google Scholar]
  5. Baldani, J. I., Baldani, V. L. D., Seldin, L. & Döbereiner, J. ( 1986; ). Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 30, 86–93.
    [Google Scholar]
  6. Baldani, J. I., Pot, B., Kirchhof, G. & 8 other authors ( 1996; ). Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a mild plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. Int J Syst Bacteriol 46, 802–810.[CrossRef]
    [Google Scholar]
  7. Brosius, J., Dull, T. L., Sleeter, D. D. & Noller, H. F. ( 1981; ). Gene organization of primary structure of a ribosomal operon from Escherichia coli. J Mol Biol 148, 107–127.[CrossRef]
    [Google Scholar]
  8. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. ( 1977; ). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461–466.[CrossRef]
    [Google Scholar]
  9. de Boer, W., Leveau, J. H., Kowalchuk, G. A., Klein Gunnewiek, P. J., Abeln, E. C., Figge, M. J., Sjollema, K., Janse, J. D. & van Veen, J. A. ( 2004; ). Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. Int J Syst Evol Microbiol 54, 857–864.[CrossRef]
    [Google Scholar]
  10. De Ley, J., Cattoir, H. & Reynaerts, A. ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef]
    [Google Scholar]
  11. Ding, L. & Yokota, A. ( 2004; ). Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol 54, 2223–2230.[CrossRef]
    [Google Scholar]
  12. Döbereiner, J. ( 1995; ). Isolation and identification of aerobic nitrogen-fixing bacteria from soil and plants. In Methods in Applied Soil Microbiology and Biochemistry, pp. 134–141. Edited by K. Alef & P. Nannipieri. London: Academic Press.
  13. Döbereiner, J., Reis, V. M., Paula, M. A. & Olivares, F. L. ( 1993; ). Endophytic diazotrophs in sugar cane, tuber plants and cereals. In New Horizons in Nitrogen Fixation, pp. 671–676. Edited by R. Palacios, J. Mora & W. E. Newton. Dordrecht: Kluwer.
  14. Elbeltagy, A., Nishioka, K., Sato, T., Suzuki, H., Ye, B., Hamada, T., Isawa, T., Mitsui, H. & Minamisawa, K. ( 2001; ). Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 67, 5285–5293.[CrossRef]
    [Google Scholar]
  15. Escara, J. F. & Hutton, J. R. ( 1980; ). Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: acceleration of the renaturation rate. Biopolymers 19, 1315–1327.[CrossRef]
    [Google Scholar]
  16. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  17. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr ( 1992; ). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166–170.[CrossRef]
    [Google Scholar]
  18. Gattinger, A., Schloter, M. & Munch, J. C. ( 2002; ). Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling. FEMS Microbiol Lett 213, 133–139.[CrossRef]
    [Google Scholar]
  19. Huß, V. A. R., Festl, H. & Schleifer, K.-H. ( 1983; ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef]
    [Google Scholar]
  20. Im, W. T., Bae, H. S., Yokota, A. & Lee, S. T. ( 2004; ). Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium. Int J Syst Evol Microbiol 54, 851–855.[CrossRef]
    [Google Scholar]
  21. Jahnke, K. D. ( 1992; ). Basic computer program for evaluation of spectroscopic DNA renaturation data from GILFORD System 2600 spectrometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61–73.[CrossRef]
    [Google Scholar]
  22. Jaspers, E. & Overmann, J. ( 2004; ). Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70, 4831–4839.[CrossRef]
    [Google Scholar]
  23. Kirchhof, G., Eckert, B., Stoffels, M., Baldani, J. I., Reis, V. M. & Hartmann, A. ( 2001; ). Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. Int J Syst Evol Microbiol 51, 157–168.
    [Google Scholar]
  24. Kloos, K., Fesefeldt, A., Gliesche, C. G. & Bothe, H. ( 1995; ). DNA-probing indicates the occurrence of denitrification and nitrogen fixation genes in Hyphomicrobium. Distribution of denitrifying and nitrogen fixing isolates of Hyphomicrobium in a sewage treatment plant. FEMS Microbiol Ecol 18, 205–213.[CrossRef]
    [Google Scholar]
  25. 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.[CrossRef]
    [Google Scholar]
  26. Ludwig, W., Strunk, O., Westram, R. & 29 other authors ( 2004; ). arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef]
    [Google Scholar]
  27. Manz, W., Amann, R., Ludwig, W., Wagner, M. & Schleifer, K.-H. ( 1992; ). Phylogenetic oligodeoxynucleotide probes for the major subclass of Proteobacteria: problems and solutions. Syst Appl Microbiol 15, 593–600.[CrossRef]
    [Google Scholar]
  28. Martinez-Murcia, A. J., Benlloch, S. & Collins, M. D. ( 1992; ). Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA–DNA hybridizations. Int J Syst Bacteriol 42, 412–421.[CrossRef]
    [Google Scholar]
  29. Mesbah, M. & Whitman, W. B. ( 1989; ). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr 479, 297–306.[CrossRef]
    [Google Scholar]
  30. Olivares, F. L., James, E. K., Baldani, J. I. & Döbereiner, J. ( 1997; ). Infection of mottled stripe disease-susceptible and resistant sugar cane varieties by the endophytic diazotroph Herbaspirillum. New Phytol 135, 723–737.[CrossRef]
    [Google Scholar]
  31. Olsen, G. J., Matsuda, H., Hagström, R. & Overbeek, R. ( 1994; ). fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10, 41–48.
    [Google Scholar]
  32. Rossello-Mora, R. & Amann, R. ( 2001; ). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39–67.[CrossRef]
    [Google Scholar]
  33. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  34. Schmid, M., Baldani, J. I. & Hartmann, A. ( 2005; ). The Genus Herbaspirillum. In The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community, 3rd edn, release 3.19. Edited by M. Dworkin. New York: Springer. http://link.springer-ny.com/link/service/books/10125/
  35. 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.[CrossRef]
    [Google Scholar]
  36. Stoltzfus, J. R., So, R., Malarvithi, P. P., Ladha, J. K. & de Bruijn, F. J. ( 1997; ). Isolation of endophytic bacteria from rice and assessment of their potential for supplying rice with biologically fixed nitrogen. Plant Soil 194, 25–36.[CrossRef]
    [Google Scholar]
  37. Strunk, O. & Ludwig, W. ( 1997; ). arb: a software environment for sequence data. http://www.arb-home.de/
  38. Valverde, A., Velázquez, E., Gutiérrez, C., Cervantes, E., Ventosa, A. & Igual, J.-M. ( 2003; ). Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris. Int J Syst Evol Microbiol 53, 1979–1983.[CrossRef]
    [Google Scholar]
  39. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
  40. Zehr, J. P. & McReynolds, L. A. ( 1989; ). Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55, 2522–2526.
    [Google Scholar]
  41. Zelles, L. & Bai, Q. Y. ( 1993; ). Fractionation of fatty acids derived from soil lipids by soil phase extraction and their quantitative analysis by GC-MS. Soil Biol Biochem 25, 130–134.
    [Google Scholar]
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vol. , part 6, pp. 1341 - 1348

Similarity matrix based on 16S and 23S rRNA gene sequences of species. [PDF](17 KB)



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