1887

Abstract

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated NF2-5-3, was isolated from a paddy soil in Anseong city, Republic of Korea. This bacterium was characterized to determine its taxonomic position using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NF2-5-3 had a close relationship with, and was related most closely to, members of the genus Paraburkholderia , namely Paraburkholderia caribensis MWAP64 (98.8 % similarity), P. sabiae Br3407 (98.8 %), P. hospita LMG 20598 (98.5 %), P. terrae NBRC 100964 (98.3 %) and P. phymatum STM815 (98.1 %). Growth of strain NF2-5-3 occurred at 15–37 °C, at pH 6.0–8.0 and at NaCl concentrations of 0–2 % (w/v). The major respiratory quinone was ubiquinone 8 (Q-8) and the major fatty acids were C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C17 : 0 cyclo and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, unidentified aminophospholipids, unidentified aminolipids and unidentified polar lipids. The G+C content of the genomic DNA was 64.2 mol%. DNA–DNA relatedness values between strain NF2-5-3 and its closest phylogenetic neighbours were much lower than 70 %. Strain NF2-5-3 could be differentiated phylogenetically and phenotypically from recognized species of the genus Paraburkholderia . The isolate therefore represents a novel species, for which the name Paraburkholderia azotifigens sp. nov. is proposed, with NF2-5-3 (=KACC 18968=LMG 29961) as the type strain.

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2017-11-29
2019-12-08
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References

  1. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H et al. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992; 36: 1251– 1275 [CrossRef] [PubMed]
    [Google Scholar]
  2. Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int J Syst Evol Microbiol 2016; 66: 2836– 2846 [CrossRef] [PubMed]
    [Google Scholar]
  3. Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Frontiers in genetics 2015; 5: 429
    [Google Scholar]
  4. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47: 590– 592 [CrossRef] [PubMed]
    [Google Scholar]
  5. Gao Z, Yuan Y, Xu L, Liu R, Chen M et al. Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation. Int J Syst Evol Microbiol 2016; 66: 4185– 4190 [CrossRef] [PubMed]
    [Google Scholar]
  6. Lv YY, Chen MH, Xia F, Wang J, Qiu LH. Paraburkholderia pallidirosea sp. nov., isolated from a monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2016; 66: 4537– 4542 [CrossRef] [PubMed]
    [Google Scholar]
  7. Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E et al. Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp. Int J Syst Evol Microbiol 2013; 63: 435– 441 [CrossRef] [PubMed]
    [Google Scholar]
  8. Chen WM, James EK, Coenye T, Chou JH, Barrios E et al. Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 2006; 56: 1847– 1851 [CrossRef] [PubMed]
    [Google Scholar]
  9. Cavalcante VA, Dobereiner J. A new acid-tolerant nitrogen-fixing bacterium associated with sugarcane. Plant Soil 1988; 108: 23– 31 [CrossRef]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  11. Kim JK, Kang MS, Park SC, Kim KM, Choi K et al. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2015; 53: 435– 441 [CrossRef] [PubMed]
    [Google Scholar]
  12. Yoon SH, Ha SM, 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 [CrossRef] [PubMed]
    [Google Scholar]
  13. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876– 4882 [CrossRef] [PubMed]
    [Google Scholar]
  14. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41: 95– 98
    [Google Scholar]
  15. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983; [Crossref]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [PubMed]
    [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  18. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725– 2729 [CrossRef] [PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  20. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44: 992– 993 [PubMed]
    [Google Scholar]
  21. Weon HY, Kim BY, Joa JH, Son JA, Song MH et al. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 2008; 58: 93– 96 [CrossRef] [PubMed]
    [Google Scholar]
  22. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th ed. CA: Pearson Education Inc., Benjamin Cummings; 2002
    [Google Scholar]
  23. Atlas RM. Handbook of Microbiological Media. In Parks LC. (editor) Boca Raton, FL: CRC Press; 1993
  24. Ten LN, Im WT, Kim MK, Kang MS, Lee ST. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 2004; 56: 375– 382 [CrossRef] [PubMed]
    [Google Scholar]
  25. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
    [Google Scholar]
  26. Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 2002; 52: 607– 616 [CrossRef] [PubMed]
    [Google Scholar]
  27. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990; pp. 199– 204
    [Google Scholar]
  28. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42: 457– 469 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef]
    [Google Scholar]
  30. Moore DD, Dowhan D. Preparation and Analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York, NY: Wiley; 1995; pp. 2– 11
    [Google Scholar]
  31. 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 [CrossRef]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37: 463– 464 [Crossref]
    [Google Scholar]
  34. Achouak W, Christen R, Barakat M, Martel MH, Heulin T. Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique. Int J Syst Bacteriol 1999; 49: 787– 794 [CrossRef] [PubMed]
    [Google Scholar]
  35. Chen WM, de Faria SM, Chou JH, James EK, Elliott GN et al. Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 2008; 58: 2174– 2179 [CrossRef] [PubMed]
    [Google Scholar]
  36. Goris J, Dejonghe W, Falsen E, de Clerck E, Geeraerts B et al. Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov. Syst Appl Microbiol 2002; 25: 340– 352 [CrossRef] [PubMed]
    [Google Scholar]
  37. Yang HC, Im WT, Kim KK, An DS, Lee ST. Burkholderia terrae sp. nov., isolated from a forest soil. Int J Syst Evol Microbiol 2006; 56: 453– 457 [CrossRef] [PubMed]
    [Google Scholar]
  38. Vandamme P, Goris J, Chen WM, de Vos P, Willems A. Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst Appl Microbiol 2002; 25: 507– 512 [CrossRef] [PubMed]
    [Google Scholar]
  39. Baek I, Seo B, Lee I, Yi H, Chun J. Burkholderia monticola sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2015; 65: 504– 509 [CrossRef] [PubMed]
    [Google Scholar]
  40. de Meyer SE, Cnockaert M, Ardley JK, Maker G, Yates R et al. Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2013; 63: 3950– 3957 [CrossRef] [PubMed]
    [Google Scholar]
  41. Aizawa T, Bao ve N, Vijarnsorn P, Nakajima M, Sunairi M. Burkholderia acidipaludis sp. nov., aluminum-tolerant bacteria isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps in South-East Asia. Int J Syst Evol Microbiol 2010; 60: 2036– 2041 [CrossRef] [PubMed]
    [Google Scholar]
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