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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 3

sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field Free

Abstract

A Gram-stain-negative bacterium, designated strain PF-30, was isolated from floodwater of a paddy field in South Korea. Strain PF-30 was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25–40 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum pH 7.0) and at salinities of 0.5–3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30 belongs to the genus , showing highest sequence similarity to TU-7 (97.1%) and less than 91.3 % similarity with other members of the family . The average nucleotide identity (ANI) and DNA–DNA relatedness between the strain PF-30 and TU-7 yielded an ANI value of 75.1 % and DNA–DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C and C 7. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30 was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is PF-30 (=KACC 19985=NBRC 113984).

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Keyword(s): Elioraea rosea sp. nov. and floodwater of a paddy field
© 2020 The Authors
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2020-02-06
2024-12-03
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References

  1. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. Int J Syst Evol Microbiol 2008; 58:773–778 [View Article]
     [Google Scholar]
  2. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2001; 51:357–363 [View Article]
     [Google Scholar]
  3. Lee H-J, Han S-I, Whang K-S. Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil. Int J Syst Evol Microbiol 2012; 62:856–859 [View Article]
     [Google Scholar]
  4. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  5. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
     [Google Scholar]
  6. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  8. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  9. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article]
     [Google Scholar]
  10. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article]
     [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  12. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  13. 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]
  14. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  15. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, -O K et al. International Committee on systematic bacteriology. Report of the ad hoc Committee on reconciliation of approches to bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  16. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Kreig NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 21–41
     [Google Scholar]
  17. Zhang J, Gu T, Zhou Y, He J, Zheng L-Q et al. Terrimonas rubra sp. nov., isolated from a polluted farmland soil and emended description of the genus Terrimonas . Int J Syst Evol Microbiol 2012; 62:2593–2597 [View Article]
     [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Manual of Method for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  19. Schwyn B, Neilands JB. Universal chemical assay for the detection and determination of siderophores. Anal Biochem 1987; 160:47–56 [View Article]
     [Google Scholar]
  20. Bric JM, Bostock RM, Silverstone SE. Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Appl Environ Microbiol 1991; 57:535–538 [View Article]
     [Google Scholar]
  21. Nautiyal CS. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 1999; 170:265–270 [View Article]
     [Google Scholar]
  22. Nagashima KV, Hiraishi A, Shimada K, Matsuura K. Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J Mol Evol 1997; 45:131–136 [View Article]
     [Google Scholar]
  23. Clayton RK. Toward the isolation of a photochemical reaction center in Rhodopseudomonas spheroides. Biochim Biophys Acta 1963; 75:312–323 [View Article]
     [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  25. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics Academic Press; 1985 pp 267–287
     [Google Scholar]
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Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field
Int J Syst Evol Microbiol 70, 2132 (2020); https://doi.org/10.1099/ijsem.0.004028
/content/journal/ijsem/10.1099/ijsem.0.004028
/content/journal/ijsem/10.1099/ijsem.0.004028
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