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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 68, Issue 8

Paenibacillus elymi sp. nov., isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea Free

Abstract

Strain KUDC6143 was isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea. Cells of this bacterial strain were Gram-positive, endospore-forming, motile and rod-shaped. The strain was capable of growth at a temperature of 25–45 °C and at a pH of 6.0–12.0; it showed an optimal growth at a temperature of 30 °C and at a pH of 7.0. In addition, it grew on a tryptic soy agar and in a tryptic soy broth containing less than 4.0 % NaCl (w/v). The cell length ranged from 2.0 to 2.7 µm. KUDC6143 was catalase-negative and oxidase-positive, and it hydrolysed starch but not casein. Its genomic G+C content was 50.3 mol%. Its major fatty acids were anteiso-C15 : 0, C16 : 0, and iso-C16 : 0. Phylogenetic analysis, based on the 16S rRNA gene sequences, showed that KUDC6143 belonged to the genus Paenibacillus , with the most closely related type strain being Paenibacillus pinihumi S23 (97.8 %). Based on its phenotypic characteristics, phylogenetic data and genetic data, strain KUDC6143 should be considered as representing a novel species of the genus Paenibacillus , for which we propose the name Paenibacillus elymi sp. nov. The type strain is KUDC6143 (=KCTC 33853=DSM 106581).

  • Received:
  • Accepted:
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Keyword(s): Dokdo Islands , Paenibacillus and Plant rhizosphere
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2018-06-29
2025-04-28
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References

  1. Ash C, Priest FG, Collins MD. 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 Leeuwenhoek 1993; 64:253–260[PubMed]
     [Google Scholar]
  2. Akaracharanya A, Lorliam W, Tanasupawat S, Lee KC, Lee JS. Paenibacillus cellulositrophicus sp. nov., a cellulolytic bacterium from Thai soil. Int J Syst Evol Microbiol 2009; 59:2680–2684 [View Article][PubMed]
     [Google Scholar]
  3. Baek SH, Yi TH, Lee ST, Im WT. Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1163–1167 [View Article][PubMed]
     [Google Scholar]
  4. Huang XF, Wang FZ, Zhang W, Li J, Ling J et al. Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean. Antonie van Leeuwenhoek 2014; 106:1089–1095 [View Article][PubMed]
     [Google Scholar]
  5. Hoon C, Soo-Young P, Choong-Min R, Kj F, Seung-Hwan P et al. Diversity of root-associated Paenibacillus spp. in winter crops from the southern part of Korea. J Microbiol Biotechnol 2005; 15:1286–1298
     [Google Scholar]
  6. Baik KS, Lim CH, Choe HN, Kim EM, Seong CN. Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 2011; 61:529–534 [View Article][PubMed]
     [Google Scholar]
  7. Wang XM, Ma S, Yang SY, Peng R, Zheng Y et al. Paenibacillus nasutitermitis sp. nov., isolated from a termite gut. Int J Syst Evol Microbiol 2016; 66:901–905 [View Article][PubMed]
     [Google Scholar]
  8. Glaeser SP, Falsen E, Busse HJ, Kämpfer P. Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 2013; 63:777–782 [View Article][PubMed]
     [Google Scholar]
  9. Scheldeman P, Goossens K, Rodriguez-Diaz M, Pil A, Goris J et al. Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. Int J Syst Evol Microbiol 2004; 54:885–891 [View Article][PubMed]
     [Google Scholar]
  10. Shimoyama T, Johari NB, Tsuruya A, Nair A, Nakayama T. Paenibacillus relictisesami sp. nov., isolated from sesame oil cake. Int J Syst Evol Microbiol 2014; 64:1534–1539 [View Article][PubMed]
     [Google Scholar]
  11. Li P, Lin W, Liu X, Li S, Luo L et al. Paenibacillus aceti sp. nov., isolated from the traditional solid-state acetic acid fermentation culture of Chinese cereal vinegar. Int J Syst Evol Microbiol 2016; 66:3426–3431 [View Article][PubMed]
     [Google Scholar]
  12. Rivas R, Mateos PF, Martínez-Molina E, Velázquez E. Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 2005; 55:405–408 [View Article][PubMed]
     [Google Scholar]
  13. De Vos P, Ludwig W, Schleifer K-H, Whitman WB. Family IV. Paenibacillaceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 3 New York: Springer; 2009 p. 269
     [Google Scholar]
  14. Ash C, Priest FG, Collins MD. Paenibacillus gen. nov. and Paenibacillus polymyxa comb. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 51. Int J Syst Evol Microbiol 1994; 44:852
     [Google Scholar]
  15. Judicial Commission of the International Committee for Systematics of Prokaryotes The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. Int J Syst Evol Microbiol 2005; 55:513 [View Article][PubMed]
     [Google Scholar]
  16. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 1997; 47:289–298 [View Article][PubMed]
     [Google Scholar]
  17. Hwang S, Park K. Terrain and landscape at Dokdo. In Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University (editors) Nature of Dokdo Daegu: Kyeongbuk University Press; 2008 pp. 54–111
     [Google Scholar]
  18. Shim SH, Ji Hyun L, Yun DJ, Choo CO. Petrological Characteristics of Volcaniclasts and Explosive Activity within the Massive Tuff Breccia Formation, Dokdo Island, Korea Seoul: The Geological Society of Korea; 2010
     [Google Scholar]
  19. Jung S-Y, Byun J-G, Park S-H, Oh S-H, Yang J-C et al. The study of distribution characteristics of vascular and naturalized plants in Dokdo, South Korea. J Asia Pac Biodivers 2014; 7:e197e205 [View Article]
     [Google Scholar]
  20. Yoon JH, Kang SJ, Lee SY, Lee MH, Oh TK. Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1833–1837 [View Article][PubMed]
     [Google Scholar]
  21. Hwang YJ, Ghim SY. Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea. Int J Syst Evol Microbiol 2017; 67:1039–1045 [View Article][PubMed]
     [Google Scholar]
  22. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48:187–194 [View Article][PubMed]
     [Google Scholar]
  23. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [View Article][PubMed]
     [Google Scholar]
  24. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  25. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  26. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  29. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Biol 1969; 18:1–32 [View Article]
     [Google Scholar]
  30. Felsenstein J. 2008; PHYLIP (Phylogeny inference package) version 3.696. http://evolution.genetics.washington.edu/phylip.html
  31. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969 pp. 21–132
     [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  33. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  34. Perrière G, Gouy M. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 1996; 78:364–369 [View Article][PubMed]
     [Google Scholar]
  35. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual New York: Cold Spring Harbor Laboratory Press; 2001
     [Google Scholar]
  36. Shin Y-K, Lee J-S, Kim H-J, Joo W-H, Le J et al. Microbial DNA base composition (G+C mol%) and its taxonomic implications. Kor J Life Sci 1996; 6:72–77
     [Google Scholar]
  37. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  38. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [View Article]
     [Google Scholar]
  39. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  40. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  41. Smibert RM, Krieg NR. Phenotypic characterization. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  42. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  43. Shin YK, Lee J, Chun C, Kim H, Park Y. Notes: Isoprenoid Quinone Profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 1996; 6:68–69
     [Google Scholar]
  44. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: Microbial ID; 1990
     [Google Scholar]
  45. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  46. Kawamoto I, Oka T, Nara T. Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms. J Bacteriol 1981; 146:527–534[PubMed]
     [Google Scholar]
  47. Schumann P. 5- Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  48. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006; 56:781–786 [View Article][PubMed]
     [Google Scholar]
  49. Kittiwongwattana C, Thawai C. Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis). Int J Syst Evol Microbiol 2015; 65:107–112 [View Article][PubMed]
     [Google Scholar]
  50. Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC et al. Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis. Int J Syst Evol Microbiol 2009; 59:1342–1347 [View Article][PubMed]
     [Google Scholar]
  51. Kim BC, Lee KH, Kim MN, Kim EM, Rhee MS et al. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora. J Microbiol 2009; 47:530–535 [View Article][PubMed]
     [Google Scholar]
  52. Wang M, Yang M, Zhou G, Luo X, Zhang L et al. Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:2081–2085 [View Article][PubMed]
     [Google Scholar]
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Paenibacillus elymi sp. nov., isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea
Int J Syst Evol Microbiol 68, 2615 (2018); https://doi.org/10.1099/ijsem.0.002892
/content/journal/ijsem/10.1099/ijsem.0.002892
/content/journal/ijsem/10.1099/ijsem.0.002892
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