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f Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov.

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Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov., Page 1 of 1

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  • A straw-coloured, Gram-staining-negative, aerobic, motile and rod-shaped bacterium, designated strain K-1-15, was isolated from reclaimed grassland soil from Biratnagar, Morang, Nepal. This strain was non-spore-forming, catalase-negative and oxidase-positive. It was able to grow at 10–45 °C, pH 6.5–9.5 and 0–1.5 % (w/v) NaCl concentration. This strain was taxonomically characterized by a polyphasic approach. Based on the results of 16S rRNA gene sequence analysis, K-1-15 formed a distinct lineage within the family Oxalobacteraceae and was most closely related to members of the genera Herbaspirillum (96.99–95.34 % sequence similarity), Noviherbaspirillum (96.72–95.45 % sequence similarity) and Paraherbaspirillum (95.85 % sequence similarity). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids of K-1-15 were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16  :   0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C10 : 0 3-OH, and iso-C16 : 0. The genomic DNA G+C content of this novel strain was 65.2 mol %. The DNA–DNA relatedness between K-1-15 and Herbaspirillum massiliense DSM 25712 and Noviherbaspirillum soli LMG 26149 were 18.3 and 13.7 % repectively. On the basis of the results of morphological, physiological, chemotaxonomic and phylogenetic analyses, K-1-15 represents a novel species of the genus Noviherbaspirillum in the family Oxalobacteraceae , for which the name Noviherbaspirillum agri sp. nov. is proposed. The type strain is K-1-15 (=KEMB 9005-422=KACC 18909=JCM 31463). Based on new data obtained in this study, we also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. (type strain JC206=CSUR P159=DSM 25712).

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain K-25 1-15 is KX129821.

  • Five supplementary figures are available with the online Supplementary Material.

© 2017 IUMS | Published by the Microbiology Society

  • 1. Baldani JI, Baldani VLD, Seldin L, Dobereiner J. Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 1986;36:86–93 [CrossRef]
     [Google Scholar]
  • 2. Baldani JI, Pot B, Kirchhof G, Falsen E, Baldani VL et al. Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a milk plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. Int J Syst Bacteriol 1996;46:802–810 [CrossRef][PubMed]
     [Google Scholar]
  • 3. Carro L, Rivas R, León-Barrios M, González-Tirante M, Velázquez E et al. Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum. Int J Syst Evol Microbiol 2012;62:1300–1306 [CrossRef][PubMed]
     [Google Scholar]
  • 4. Lin SY, Hameed A, Arun AB, Liu YC, Hsu YH et al. Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis. Int J Syst Evol Microbiol 2013;63:4100–4107 [CrossRef][PubMed]
     [Google Scholar]
  • 5. Kim SJ, Moon JY, Weon HY, Hong SB, Seok SJ et al. Noviherbaspirillum suwonense sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2014;64:1552–1558 [CrossRef][PubMed]
     [Google Scholar]
  • 6. Pham VH, Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol 2012;30:475–484 [CrossRef][PubMed]
     [Google Scholar]
  • 7. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016;66:3170–3176 [CrossRef][PubMed]
     [Google Scholar]
  • 8. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981; pp.21–33
     [Google Scholar]
  • 9. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining Gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995;61:3756–3758[PubMed]
     [Google Scholar]
  • 10. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016;66:4347–4354 [CrossRef][PubMed]
     [Google Scholar]
  • 11. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. et al (editors) Methods for General and Molecular Bacteriology, 3rd ed.. Washington, DC: American Society for Microbiology; 2007; pp.309–329
     [Google Scholar]
  • 12. Sorokin DY. Is there a limit for high-pH life?. Int J Syst Evol Microbiol 2005;55:1405–1406 [CrossRef][PubMed]
     [Google Scholar]
  • 13. Zhang DC, Redzic M, Schinner F, Margesin R. Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2011;61:2186–2190 [CrossRef][PubMed]
     [Google Scholar]
  • 14. Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016;66:4621–4627 [CrossRef][PubMed]
     [Google Scholar]
  • 15. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. et al (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007; pp.330–393
     [Google Scholar]
  • 16. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
     [Google Scholar]
  • 17. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  • 18. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
     [Google Scholar]
  • 19. Naziri D, Hamidi M, Hassanzadeh S, Tarhriz V, Maleki Zanjani B et al. Analysis of carotenoid production by Halorubum sp. TBZ126; an extremely halophilic archeon from Urmia Lake. Adv Pharm Bull 2014;4:61–67 [CrossRef][PubMed]
     [Google Scholar]
  • 20. Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016;66:308–314 [CrossRef][PubMed]
     [Google Scholar]
  • 21. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–218 [CrossRef]
     [Google Scholar]
  • 22. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008;74:2461–2470 [CrossRef][PubMed]
     [Google Scholar]
  • 23. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 24. 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]
  • 25. 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]
  • 26. 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]
  • 27. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
     [Google Scholar]
  • 28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
     [Google Scholar]
  • 29. 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]
  • 30. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 31. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
     [Google Scholar]
  • 32. 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]
  • 33. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
     [Google Scholar]
  • 34. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–203[CrossRef]
     [Google Scholar]
  • 35. Busse HJ, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
     [Google Scholar]
  • 36. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997;47:698–708 [CrossRef]
     [Google Scholar]
  • 37. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007;57:572–576 [CrossRef][PubMed]
     [Google Scholar]
  • 38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  • 39. 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]
  • 40. 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]
  • 41. Dӧbereiner J. Isolation and identification of aerobic nitrogen-fixing bacteria from soil and plants. In Alef K, Nannipieri P. (editors) Methods in Applied Soil Microbiology and Biochemistry London: Academic Press; 1995; pp.134–141
     [Google Scholar]
  • 42. Baldani JI, Reis VM, Videira SS, Boddey LH, Baldani VLD. The art of isolating nitrogen-fixing bacteria from non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists. Plant Soil 2014;384:413–431 [CrossRef]
     [Google Scholar]
  • 43. Pimentel JP, Olivares F, Pitard RM, Urquiaga S, Akiba F et al. Dinitrogen fixation and infection of grass leaves by Pseudomonas rubrisubalbicans and Herbaspirillum seropedicae. Plant Soil 1991;137:61–65 [CrossRef]
     [Google Scholar]
  • 44. Anandham R, Kim SJ, Moon JY, Weon HY, Kwon SW. Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil. J Microbiol 2013;51:262–267 [CrossRef][PubMed]
     [Google Scholar]
  • 45. Baldani J I, Rouws L, Cruz LM, Olivares FL, Schmid M et al. The family Oxalobacteraceae. In Rosenberg R, DeLong EF, Lory S, Stackebrandt E, Thompson F. et al (editors) The Prokaryotes- Alphaproteobacteria and Betaproteobacteria, 4th ed. Berlin Heidelberg: Springer; 2014; pp.919–974[CrossRef]
     [Google Scholar]
  • 46. 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 [CrossRef]
     [Google Scholar]
  • 47. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241–250 [CrossRef][PubMed]
     [Google Scholar]
  • 48. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
     [Google Scholar]
  • 49. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012;7:200–209 [CrossRef]
     [Google Scholar]
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