sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Free

Abstract

A bacterial strain designated SBR5 was isolated from the rhizosphere of . A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genus , being most closely related to RSA19 (98.1 % similarity). The isolate was a Gram-reaction-variable, motile, facultatively anaerobic bacterium, with spores in a terminal position in cells. Starch was utilized and dihydroxyacetone and catalase were produced. Strain SBR5 displayed plant-growth-promoting rhizobacteria characteristics: the ability to fix nitrogen and to produce siderophores and indole-3-acetic acid. The DNA G+C content was 55.1 mol%. Chemotaxonomic analysis of the isolated strain revealed that MK-7 was the predominant menaquinone, while the major fatty acid was anteiso-C. DNA–DNA hybridization values between strain SBR5 and RSA19, TOD45 and KK19 were 43, 35 and 28 %, respectively. These DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain SBR5 should be considered as the nitrogen-fixing type strain of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SBR5 (=CCGB 1313 =CECT 7330).

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2010-01-01
2024-03-28
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References

  1. Ash C., Priest F. G., Collins M. D. 1994 Paenibacillus gen. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB , List no. 51. Int J Syst Bacteriol 44, 852 [CrossRef]
  2. Berge O., Guinebretiére M., Achouak W., Normand P., Heulin T. 2002; Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 52:607–616
    [Google Scholar]
  3. Borges F. P., Wiltuschnig R. C., Tasca T., de Carli G. A. 2004; Scanning electron microscopy study of Tritrichimonas augusta . Parasitol Res 94:158–161 [CrossRef]
    [Google Scholar]
  4. Choi J. H., Im W. T., Yoo J. S., Lee S. M., Moon D. S., Kim H. J., Rhee S. K., Roh D. H. 2008; Paenibacillus donghaensis sp. nov., a xylan-degrading and nitrogen-fixing bacterium isolated from East Sea sediment. J Microbiol Biotechnol 18:189–193
    [Google Scholar]
  5. Chun J., Lee J. H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 2007; EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261 [CrossRef]
    [Google Scholar]
  6. Claus D., Berkeley R. C. W. 1986; Genus Bacillus Cohn 1872,174AL . In Bergey's Manual of Systematic Bacteriology , 2nd edn. pp 1105–1139 Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  7. 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]
  8. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology . pp 21–33 Edited by Gerdhardt 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;
  9. Elo S., Suominen I., Kämpfer P., Juhanoja J., Salkinoja-Salonen M., Haahtela K. 2001; Paenibacillus borealis sp. nov., a nitrogen-fixing species isolated from spruce forest humus in Finland. Int J Syst Evol Microbiol 51:535–545
    [Google Scholar]
  10. Felsenstein J. 1983; Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14:313–333 [CrossRef]
    [Google Scholar]
  11. Glickmann E., Dessaux Y. 1995; A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61:793–796
    [Google Scholar]
  12. Grau F. H., Wilson P. W. 1962; Physiology of nitrogen-fixation by Bacillus polymyxa . J Bacteriol 83:490–496
    [Google Scholar]
  13. Helbig J. 2001; Biological control of Botrytis cinerea Pers. ex Fr. in strawberry by Paenibacillus polymyxa (isolate 18191. J Phytopathol 149:265–273 [CrossRef]
    [Google Scholar]
  14. Keeney D. R., Bremner J. M. 1966; A chemical index of soil nitrogen availability. Nature 211:892–893 [CrossRef]
    [Google Scholar]
  15. 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]
    [Google Scholar]
  16. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; mega2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245 [CrossRef]
    [Google Scholar]
  17. Lebuhn M., Heulin T., Hartmann A. 1997; Production of auxin and other indolic and phenolic compounds by Paenibacillus polymyxa strains isolated from different proximity to plant roots. FEMS Microbiol Ecol 22:325–334 [CrossRef]
    [Google Scholar]
  18. Ma Y. C., Chen S. F. 2008; Paenibacillus forsythiae sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of Forsythia mira . Int J Syst Evol Microbiol 58:319–323 [CrossRef]
    [Google Scholar]
  19. Ma Y., Xia Z., Liu X., Chen S. 2007a; Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs. Int J Syst Evol Microbiol 57:6–11 [CrossRef]
    [Google Scholar]
  20. Ma Y., Zhang J., Chen S. 2007b; Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans . Int J Syst Evol Microbiol 57:873–877 [CrossRef]
    [Google Scholar]
  21. MacFaddin J. F. 2000 Biochemical Tests for Identification of Medical Bacteria , 3rd edn. Philadelphia, PA: Lippincott, Williams & Wilkins;
    [Google Scholar]
  22. MacKenzie S. L. 1987; Gas chromatographic analysis of amino acids as the N -heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160
    [Google Scholar]
  23. MIDI 2001 Sherlock Microbial Identification System Operating Manual , version 4.0 Newark, DE: MIDI, Inc;
    [Google Scholar]
  24. Montefusco A., Nakamura L. K., Labeda D. P. 1993; Bacillus peoriae sp. nov. Int J Syst Bacteriol 43:388–390 [CrossRef]
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. Reva O. N., Vyunitskaya V. A., Reznik S. R., Kozachko I. A., Smirnov V. V. 1995; Antibiotic susceptibility as a taxonomic characteristic of the genus Bacillus . Int J Syst Evol Microbiol 45:409–411
    [Google Scholar]
  27. Rivas R., Sánchez M., Trujillo M. E., Zurdo-Piñeiro J. L., Mateos P. F., Martínez-Molina E., Velázquez E. 2003; Xylanimonas cellulosilytica gen. nov., sp. nov. a xylanolytic bacterium isolated from a decayed tree ( Ulmus nigra . Int J Syst Evol Microbiol 53:99–103 [CrossRef]
    [Google Scholar]
  28. Rodríguez-Díaz M., Lebbe L., Rodelas B., Heyrman J., de Vos P., Logan N. A. 2005; Paenibacillus wynnii sp. nov., a novel species harbouring the nifH gene, isolated from Alexander Island, Antarctica. Int J Syst Evol Microbiol 55:2093–2099 [CrossRef]
    [Google Scholar]
  29. Rosado A. S., Seldin L., Wolters A. C., van Elsas J. D. 1996; Quantitative 16S rDNA-targeted polymerase chain reaction and oligonucleotide hybridization for the detection of Paenibacillus azotofixans in soil and the wheat rhizosphere. FEMS Microbiol Ecol 19:153–164 [CrossRef]
    [Google Scholar]
  30. Roux V., Raoult D. 2004; Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov, isolated from blood cultures. Int J Syst Evol Microbiol 54:1049–1054 [CrossRef]
    [Google Scholar]
  31. Rzhetsky A., Nei M. 1993; Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095
    [Google Scholar]
  32. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  33. Sambrook J., Russell D. W. 2001 Molecular Cloning: A Laboratory Manual , 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  34. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
    [Google Scholar]
  35. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477
    [Google Scholar]
  36. Schwyn B., Neilands J. B. 1987; Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56 [CrossRef]
    [Google Scholar]
  37. Seldin L., van Elsas J. D., Penido E. G. C. 1983; Bacillus nitrogen fixers from Brazilian soils. Plant Soil 70:243–255 [CrossRef]
    [Google Scholar]
  38. Shida O., Takagi H., Kadowaki K., Nakamura L. K., Komagata K. 1997; Emended description of Paenibacillus amylolyticus and description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov. Int J Syst Bacteriol 47:299–306 [CrossRef]
    [Google Scholar]
  39. Suominen I., Spröer C., Kämpfer P., Rainey F. A., Lounatmaa K., Salkinoja-Salonen M. 2003; Paenibacillus stellifer sp. nov., a cyclodextrin-producing species isolated from paperboard. Int J Syst Evol Microbiol 53:1369–1374 [CrossRef]
    [Google Scholar]
  40. 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]
    [Google Scholar]
  41. Timmusk S., Wagner E. G. 1999; The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant Microbe Interact 12:951–959 [CrossRef]
    [Google Scholar]
  42. Timmusk S., Nicander B., Granhall U., Tillberg E. 1999; Cytokinin production by Paenibacillus polymyxa . Soil Biol Biochem 31:1847–1852 [CrossRef]
    [Google Scholar]
  43. von der Weid I., Duarte G. F., van Elsas J. D., Seldin L. 2002; Paenibacillus brasilensis sp. nov., a new nitrogen-fixing species isolated from the maize rhizosphere in Brazil. Int J Syst Evol Microbiol 52:2147–2153 [CrossRef]
    [Google Scholar]
  44. von der Weid I., Alviano D. S., Santos A. L., Soares R. M., Alviano C. S., Seldin L. 2003; Antimicrobial activity of Paenibacillus peoriae strain NRRL BD-62 against a broad spectrum of phytopathogenic bacteria and fungi. J Appl Microbiol 95:1143–1151 [CrossRef]
    [Google Scholar]
  45. 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; 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]
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