1887

Abstract

A novel endophytic bacterium, strain 1DrF-4, isolated from rice roots, was characterized on the basis of its phenotypic characteristics and genotypic information. The novel strain was Gram-positive-staining, endospore-forming, facultatively anaerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1DrF-4 formed a monophyletic clade within the genus . The most phylogenetically related species was KACC 17472, with which strain 1DrF-4 showed 16S rRNA gene sequence similarity of 95.2 %. 16S rRNA gene sequence similarities with type strains of other species of the genus were less than 95 %. The predominant cellular fatty acids were anteiso-C (61.1 %) and C (11.1 %), which is one of the characteristic traits of the genus The quinone system contained exclusively menaquinone MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid and an unknown phospholipid. The DNA G+C content was 50.16 mol%, which was within the range reported for species of the genus . Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain 1DrF-4 (=ACCC 19927=JCM 30486) represents a novel species of the genus , for which the name sp. nov. is proposed.

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2016-12-01
2020-01-22
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References

  1. Ash C., Priest F. G., Collins M. D.. 1993; Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek64:253–260[PubMed][CrossRef]
    [Google Scholar]
  2. Beneduzi A., Ambrosini A., Passaglia L. M.. 2012; Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents. Genet Mol Biol35:1044–1051 [CrossRef][PubMed]
    [Google Scholar]
  3. Berge O., Guinebretière M. H., 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 Microbiol52:607–616 [CrossRef][PubMed]
    [Google Scholar]
  4. Carro L., Flores-Félix J. D., Cerda-Castillo E., Ramírez-Bahena M. H., Igual J. M., Tejedor C., Velázquez E., Peix A. 2013; Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol63:4433–4438 [CrossRef][PubMed]
    [Google Scholar]
  5. Dong X. Z., Cai M. Y.. (editors) 2001; Determination of biochemical properties. In Manual for the Systematic Identification of General Bacteria pp370–398 Beijing: Science Press (in Chinese);
    [Google Scholar]
  6. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  7. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791 [CrossRef]
    [Google Scholar]
  8. Jin H. J., Lv J., Chen S. F.. 2011; Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica. Int J Syst Evol Microbiol61:767–771 [CrossRef][PubMed]
    [Google Scholar]
  9. Kim B. C., Jeong W. J., Kim D. Y., Oh H. W., Kim H., Park D. S., Park H. M., Bae K. S.. 2009; Paenibacillus pueri sp. nov., isolated from Pu'er tea. Int J Syst Evol Microbiol59:1002–1006 [CrossRef][PubMed]
    [Google Scholar]
  10. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim T. S., Han J. H., Joung Y., Kim S. B.. 2015a; Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants. Int J Syst Evol Microbiol65:2717–2725 [CrossRef][PubMed]
    [Google Scholar]
  12. Kim H. S., Srinivasan S., Lee S. S.. 2015b; Paenibacillus alba nov., isolated from peat soil. Curr Microbiol70:865–870 [CrossRef][PubMed]
    [Google Scholar]
  13. Kloepper J. W., Leong J., Teintze M., Schroth M. N.. 1980; Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature286:885–886 [CrossRef]
    [Google Scholar]
  14. Komagata K., Suzuki K. I. 1988; 4 lipid and cell-wall analysis in bacterial systematics. Method Microbiol19:161–207[CrossRef]
    [Google Scholar]
  15. Lane D. J.. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp115–175 Edited by Stackebrandt E., Goodfellow M.. Chichester: Wiley;
    [Google Scholar]
  16. Lechevalier M. P., Lechevalier H. A.. 1980; The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, Society for Industrial Microbiology pp227–291 . Edited by Dietz A., Thayer D. W., Fairfax V. A.. Utrecht: SIM Special Publication;
    [Google Scholar]
  17. Liu Y., Liu L., Qiu F., Schumann P., Shi Y., Zou Y., Zhang X., Song W.. 2010; Paenibacillus hunanensis sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol60:1266–1270 [CrossRef][PubMed]
    [Google Scholar]
  18. Liu Y., Zhai L., Wang R., Zhao R., Zhang X., Chen C., Cao Y., Cao Y., Xu T. et al. 2015; Paenibacillus zeae sp. nov., isolated from maize (Zea mays L.) seeds. Int J Syst Evol Microbiol65:4533–4538 [CrossRef][PubMed]
    [Google Scholar]
  19. Marmur J., Doty P.. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118 [CrossRef][PubMed]
    [Google Scholar]
  20. Ming H., Nie G. X., Jiang H. C., Yu T. T., Zhou E. M., Feng H. G., Tang S. K., Li W. J.. 2012; Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie Van Leeuwenhoek102:297–305[CrossRef]
    [Google Scholar]
  21. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods2:233–241 [CrossRef]
    [Google Scholar]
  22. Moon J., Kim J.. 2014; Isolation of paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-do, Korea. J Microbiol52:273–277 [CrossRef][PubMed]
    [Google Scholar]
  23. Oh H. W., Kim B. C., Lee K. H., Kim D. Y., Park D. S., Park H. M., Bae K. S.. 2008; Paenibacillus camelliae sp. nov., isolated from fermented leaves of Camellia sinensis. J Microbiol46:530–534 [CrossRef][PubMed]
    [Google Scholar]
  24. Ruan Z., Wang Y., Song J., Jiang S., Wang H., Li Y., Zhao B., Jiang R., Zhao B.. 2014; Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia. Int J Syst Evol Microbiol64:518–521 [CrossRef][PubMed]
    [Google Scholar]
  25. Rzhetsky A., Nei M.. 1992; A simple method for estimating and testing minimum evolution trees. Mol Biol Evol9:945–967
    [Google Scholar]
  26. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  27. Sasser M.. 1990; Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101. Newark, DE: MIDI Inc;
    [Google Scholar]
  28. Schleifer K. H.. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol18:123–156[CrossRef]
    [Google Scholar]
  29. Smerda J., Sedlácek I., Pácová Z., Durnová E., Smísková A., Havel L.. 2005; Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L. Int J Syst Evol Microbiol55:2351–2354 [CrossRef][PubMed]
    [Google Scholar]
  30. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  31. Wang Y., Shi Y., Li B., Shan C., Ibrahim M., Jabeen A., Xie G., Sun G.. 2012; Phosphate solubilization of Paenibacillus polymyxa and Paenibacillus macerans from mycorrhizal and non-mycorrhizal cucumber plants. Afr J Microbiol Res6:4567–4573
    [Google Scholar]
  32. Zhang X., Sun L., Ma X., Sui X. H., Jiang R.. 2011; Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. Int J Syst Evol Microbiol61:2425–2459 [CrossRef][PubMed]
    [Google Scholar]
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