1887

Abstract

A bacterial strain named BSTT44 was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7 % identity with respect to that of its closest relative, E-3, and the next most closely related type strains were those of , with 99.6 % similarity, , with 99.2 % similarity, and , with 99.0 % similarity; these results indicate that BSTT44 should be classified within the genus . Analysis of the housekeeping genes , and confirmed its phylogenetic affiliation and showed identities lower than 92 % in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar–subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C, Cω7 and summed feature 3 (Cω7 and/or Cω6). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5–9.The DNA G+C content was 60.2 mol%. DNA–DNA hybridization results showed less than 48 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus , for which the name sp. nov. is proposed. The type strain is BSTT44 ( = LMG 28456 = CECT 8691).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000230
2015-07-01
2019-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/7/2110.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000230&mimeType=html&fmt=ahah

References

  1. Ait Tayeb L. , Ageron E. , Grimont F. , Grimont P.A.D. . ( 2005;). Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156: 763–773 [CrossRef] [PubMed].
    [Google Scholar]
  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 [CrossRef] [PubMed].
    [Google Scholar]
  3. Aravind R. , Kumar A. , Eapen S.J. , Ramana K.V. . ( 2009;). Endophytic bacterial flora in root and stem tissues of black pepper (Piper nigrum L.) genotype: isolation, identification and evaluation against Phytophthora capsici . Lett Appl Microbiol 48: 58–64 [CrossRef] [PubMed].
    [Google Scholar]
  4. Berg G. , Krechel A. , Ditz M. , Sikora R. , Ulrich A. , Hallmann J. . ( 2005;). Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51: 215–229.[CrossRef]
    [Google Scholar]
  5. Carrión O. , Miñana-Galbis D. , Montes M.J. , Mercadé E. . ( 2011;). Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Microbiol 61: 2401–2405 [CrossRef] [PubMed].
    [Google Scholar]
  6. Chun J. , Goodfellow M. . ( 1995;). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45: 240–245 [CrossRef] [PubMed].
    [Google Scholar]
  7. Clark L.L. , Dajcs J.J. , McLean C.H. , Bartell J.G. , Stroman D.W. . ( 2006;). Pseudomonas otitidis sp. nov., isolated from patients with otic infections. Int J Syst Evol Microbiol 56: 709–714 [CrossRef] [PubMed].
    [Google Scholar]
  8. Collins M.D. . ( 1985;). Analysis of isoprenoid quinones. Methods Microbiol 18: 329–366 [CrossRef].
    [Google Scholar]
  9. Collins M.D. , Jones D. . ( 1981;). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45: 316–354 [PubMed].
    [Google Scholar]
  10. Diallo S. , Crepin A. , Barbey C. , Orange N. , Burini J.F. , Latour X. . ( 2011;). Mechanisms and recent advances in biological control mediated through the potato rhizosphere. FEMS Microbiol Ecol 75: 351–364.[CrossRef]
    [Google Scholar]
  11. Doetsch R.N. . ( 1981;). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 21–33. Edited by Gerhardt P. , Murray R. G. E. , Costilow R. N. , Nester E. W. , Wood W. A. , Krieg N. R. , Phillips G. B. . Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  12. Ezaki T. , Hashimoto Y. , Yabuuchi E. . ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39: 224–229 [CrossRef].
    [Google Scholar]
  13. Garbeva P. , van Overbeek L.S. , van Vuurde J.W.L. , van Elsas J.D. . ( 2001;). Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments. Microb Ecol 41: 369–383.[CrossRef]
    [Google Scholar]
  14. Hildebrand D.C. , Palleroni N.J. , Hendson M. , Toth J. , Johnson J.L. . ( 1994;). Pseudomonas flavescens sp. nov., isolated from walnut blight cankers. Int J Syst Bacteriol 44: 410–415 [CrossRef] [PubMed].
    [Google Scholar]
  15. Kim O.S. , Cho Y.J. , Lee K. , Yoon S.H. , Kim M. , Na H. , Park S.C. , Jeon Y.S. , Lee J.H. , other authors . ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721 [CrossRef] [PubMed].
    [Google Scholar]
  16. 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 [CrossRef] [PubMed].
    [Google Scholar]
  17. King E.O. , Ward M.K. , Raney D.E. . ( 1954;). Two simple media for the demonstration of pyocyanin and fluorescein. J Lab Clin Med 44: 301–307 [PubMed].
    [Google Scholar]
  18. Krechel A. , Faupel A. , Hallmann J. , Ulrich A. , Berg G. . ( 2002;). Potato-associated bacteria and their antagonistic potential towards plant-pathogenic fungi and the plant-parasitic nematode Meloidogyne incognita (Kofoid & White) Chitwood. Can J Microbiol 48: 772–786 [CrossRef] [PubMed].
    [Google Scholar]
  19. Mandel M. , Marmur J. . ( 1968;). Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B: 195–206 [CrossRef].
    [Google Scholar]
  20. Mendes R. , Garbeva P. , Raaijmakers J.M. . ( 2013;). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37: 634–663 [CrossRef] [PubMed].
    [Google Scholar]
  21. Molin G. , Ternström A. , Ursing J. . ( 1986;). Pseudomonas lundensis, a new bacterial species isolated from meat. Int J Syst Bacteriol 36: 339–342 [CrossRef].
    [Google Scholar]
  22. Mulet M. , Bennasar A. , Lalucat J. , García-Valdés E. . ( 2009;). An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 23: 140–147 [CrossRef] [PubMed].
    [Google Scholar]
  23. Mulet M. , Lalucat J. , García-Valdés E. . ( 2010;). DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12: 1513–1530 [PubMed].
    [Google Scholar]
  24. Mulet M. , Gomila M. , Lemaitre B. , Lalucat J. , García-Valdés E. . ( 2012;). Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov.. Syst Appl Microbiol 35: 145–149 [CrossRef] [PubMed].
    [Google Scholar]
  25. Palleroni N.J. . ( 2005;). Genus I. Pseudomonas Migula 1894, 237AL (nom. cons., Opin. 5 of the Jud. Comm. 1952, 121). . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 2B, pp. 323–379. Edited by Boone D. R. , Brenner D. J. , Castenholz R. W. , Garrity G. M. , Krieg N. R. , Staley J. T. . New York: Springer;.
    [Google Scholar]
  26. Peix A. , Berge O. , Rivas R. , Abril A. , Velázquez E. . ( 2005;). Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina. Int J Syst Evol Microbiol 55: 1107–1112 [CrossRef] [PubMed].
    [Google Scholar]
  27. Ramírez-Bahena M.H. , Cuesta M.J. , Flores-Félix J.D. , Mulas R. , Rivas R. , Castro-Pinto J. , Brañas J. , Mulas D. , González-Andrés F. , other authors . ( 2014;). Pseudomonas helmanticensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 64: 2338–2345 [CrossRef] [PubMed].
    [Google Scholar]
  28. Ramos E. , Ramírez-Bahena M.H. , Valverde A. , Velázquez E. , Zúñiga D. , Velezmoro C. , Peix A. . ( 2013;). Pseudomonas punonensis sp. nov., isolated from straw. Int J Syst Evol Microbiol 63: 1834–1839 [CrossRef] [PubMed].
    [Google Scholar]
  29. Reiter B. , Pfeifer U. , Schwab H. , Sessitsch A. . ( 2002;). Response of endophytic bacterial communities in potato plants to infection with Erwinia carotovora subsp atroseptica. Appl Environ Microbiol 68: 2261–2268.[CrossRef]
    [Google Scholar]
  30. Rivas R. , García-Fraile P. , Mateos P.F. , Martínez-Molina E. , Velázquez E. . ( 2007;). Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera . Lett Appl Microbiol 44: 181–187 [CrossRef] [PubMed].
    [Google Scholar]
  31. Rogers J.S. , Swofford D.L. . ( 1998;). A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst Biol 47: 77–89 [CrossRef] [PubMed].
    [Google Scholar]
  32. Rosenblueth M. , Martínez-Romero E. . ( 2006;). Bacterial endophytes and their interactions with hosts. Mol Plant Microbe Interact 19: 827–837 [CrossRef] [PubMed].
    [Google Scholar]
  33. Ryan R.P. , Germaine K. , Franks A. , Ryan D.J. , Dowling D.N. . ( 2008;). Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278: 1–9 [CrossRef] [PubMed].
    [Google Scholar]
  34. Saitou N. , Nei M. . ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425 [PubMed].
    [Google Scholar]
  35. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI, Inc;.
    [Google Scholar]
  36. Sessitsch A. , Reiter B. , Berg G. . ( 2004;). Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoting and antagonistic abilities. Can J Microbiol 50: 239–249.[CrossRef]
    [Google Scholar]
  37. Sturz A.V. , Matheson B.G. . ( 1996;). Populations of endophytic bacteria which influence host-resistance to Erwinia-induced bacterial soft rot in potato tubers. Plant Soil 184: 265–271.[CrossRef]
    [Google Scholar]
  38. Sturz A.V. , Christie B.R. , Matheson B.G. . ( 1998;). Associations of bacterial endophyte populations from red clover and potato crops with potential for beneficial allelopathy. Can J Microbiol 44: 162–167.[CrossRef]
    [Google Scholar]
  39. Tamaoka J. , Katayama-Fujimura Y. , Kuraishi H. . ( 1983;). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54: 31–36 [CrossRef].
    [Google Scholar]
  40. 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 [CrossRef] [PubMed].
    [Google Scholar]
  41. Thompson J.D. , Gibson T.J. , Plewniak F. , Jeanmougin F. , Higgins D.G. . ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876–4882 [CrossRef] [PubMed].
    [Google Scholar]
  42. Toro M. , Ramírez-Bahena M.H. , Cuesta M.J. , Velázquez E. , Peix A. . ( 2013;). Pseudomonas guariconensis sp. nov., isolated from rhizospheric soil. Int J Syst Evol Microbiol 63: 4413–4420 [CrossRef] [PubMed].
    [Google Scholar]
  43. Wayne L.G. , Brenner D.J. , Colwell R.R. , Grimont P.A.D. , Kandler O. , Krichevsky M.I. , Moore L.H. , Moore W.E.C. , Murray R.G.E. , other authors . ( 1987;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463–464 [CrossRef].
    [Google Scholar]
  44. Willems A. , Doignon-Bourcier F. , Goris J. , Coopman R. , de Lajudie P. , De Vos P. , Gillis M. . ( 2001;). DNA–DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51: 1315–1322 [PubMed].
    [Google Scholar]
  45. Xiao Y.P. , Hui W. , Wang Q. , Roh S.W. , Shi X.Q. , Shi J.H. , Quan Z.X. . ( 2009;). Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. Int J Syst Evol Microbiol 59: 2594–2598 [CrossRef] [PubMed].
    [Google Scholar]
  46. Yamamoto S. , Harayama S. . ( 1998;). Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB rpoD and 16S rRNA genes. Int J Syst Bacteriol 48: 813–819 [CrossRef] [PubMed].
    [Google Scholar]
  47. Yang J. , Kloepper J.W. , Ryu C.M. . ( 2009;). Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14: 1–4 [CrossRef] [PubMed].
    [Google Scholar]
  48. Yumoto I. , Kusano T. , Shingyo T. , Nodasaka Y. , Matsuyama H. , Okuyama H. . ( 2001;). Assignment of Pseudomonas sp. strain E-3 to Pseudomonas psychrophila sp. nov., a new facultatively psychrophilic bacterium. Extremophiles 5: 343–349 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000230
Loading
/content/journal/ijsem/10.1099/ijs.0.000230
Loading

Data & Media loading...

Supplementary Data



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error