1887

Abstract

Strain SPC-1 was isolated from the phyllosphere of L. var. (Lamk) Fiori (wild cardoon), a Mediterranean native plant considered to be the wild ancestor of the globe artichoke and cultivated cardoon. This Gram-stain-negative, catalase-positive, oxidase-negative, non-spore-forming, rod-shaped and non-motile strain secreted copious amounts of an exopolysaccharide, formed slimy, viscous, orange-pigmented colonies and grew optimally at around pH 6.0–6.5 and 26–30 °C in the presence of 0–0.5 % NaCl. Phylogenetic analysis based on comparisons of 16S rRNA gene sequences demonstrated that SPC-1 clustered together with species of the genus . The G+C content of the DNA (66.1 mol%), the presence of Q-10 as the predominant ubiquinone, -homospermidine as the predominant polyamine, 2-hydroxymyristic acid (C 2-OH) as the major hydroxylated fatty acid, the absence of 3-hydroxy fatty acids and the presence of sphingoglycolipid supported this taxonomic position. 16S rRNA gene sequence analysis showed that SPC-1 was most closely related to ODN7, DS-28 and C52 (98.19, 97.91 and 97.11 % sequence similarities, respectively). However, DNA–DNA hybridization analysis did not reveal any relatedness at the species level. Further differences were apparent in biochemical traits, and fatty acid, quinone and polyamine profiles leading us to conclude that strain SPC-1 represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is SPC-1 ( = JCM 17498 = ITEM 13494). A component analysis of the exopolysaccharide suggested that it represents a novel type of sphingan containing glucose, rhamnose, mannose and galactose, while glucuronic acid, which is commonly found in sphingans, was not detected.

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2013-01-01
2020-01-17
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References

  1. Bligh E. G. , Dyer W. J. . ( 1959; ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37:, 911–917. [CrossRef] [PubMed]
    [Google Scholar]
  2. Blumenkrantz N. , Asboe-Hansen G. . ( 1973; ). New method for quantitative determination of uronic acids. . Anal Biochem 54:, 484–489. [CrossRef] [PubMed]
    [Google Scholar]
  3. Brown J. K. . ( 1994; ). Bootstrap hypothesis tests for evolutionary trees and other dendrograms. . Proc Natl Acad Sci U S A 91:, 12293–12297. [CrossRef] [PubMed]
    [Google Scholar]
  4. Buonaurio R. , Stravato V. M. , Kosako Y. , Fujiwara N. , Naka T. , Kobayashi K. , Cappelli C. , Yabuuchi E. . ( 2002; ). Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. . Int J Syst Evol Microbiol 52:, 2081–2087. [CrossRef] [PubMed]
    [Google Scholar]
  5. Busse H.-J. , Kämpfer P. , Denner E. B. . ( 1999; ). Chemotaxonomic characterisation of Sphingomonas . . J Ind Microbiol Biotechnol 23:, 242–251. [CrossRef] [PubMed]
    [Google Scholar]
  6. Busse H.-J. , Denner E. B. M. , Buczolits S. , Salkinoja-Salonen M. , Bennasar A. , Kämpfer P. . ( 2003; ). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . . Int J Syst Evol Microbiol 53:, 1253–1260. [CrossRef] [PubMed]
    [Google Scholar]
  7. Busse H.-J. , Hauser E. , Kämpfer P. . ( 2005; ). Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov.. Int J Syst Evol Microbiol 55:, 2565–2569. [CrossRef] [PubMed]
    [Google Scholar]
  8. DuBois M. , Gilles K. A. , Hamilton J. K. , Rebers P. A. , Smith F. . ( 1956; ). Colorimetric method for determination of sugars and related substances. . Anal Chem 28:, 350–356. [CrossRef]
    [Google Scholar]
  9. Eguchi M. , Ostrowski M. , Fegatella F. , Bowman J. , Nichols D. , Nishino T. , Cavicchioli R. . ( 2001; ). Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. . Appl Environ Microbiol 67:, 4945–4954. [CrossRef] [PubMed]
    [Google Scholar]
  10. Ezaki T. , Hashimoto Y. , Yabuuchi E. . ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine the genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39:, 224–229. [CrossRef]
    [Google Scholar]
  11. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  12. Fialho A. M. , Moreira L. M. , Granja A. T. , Popescu A. O. , Hoffmann K. , Sá-Correia I. . ( 2008; ). Occurrence, production, and applications of gellan: current state and perspectives. . Appl Microbiol Biotechnol 79:, 889–900. [CrossRef] [PubMed]
    [Google Scholar]
  13. Galtier N. , Gouy M. , Gautier C. . ( 1996; ). seaview and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. . Comput Appl Biosci 12:, 543–548.[PubMed]
    [Google Scholar]
  14. Gehrke C. W. , Kuo K. C. T. . (editors) ( 1990; ). Chromatography and Modification of Nucleosides. Amsterdam:: Elsevier;.
    [Google Scholar]
  15. Gillis M. , De Ley J. , De Cleene M. . ( 1970; ). The determination of molecular weight of bacterial genome DNA from renaturation rates. . Eur J Biochem 12:, 143–153. [CrossRef] [PubMed]
    [Google Scholar]
  16. Kim O.-S. , Cho Y.-J. , Lee K. , Yoon S.-H. , Kim M. , Na H. , Park S.-C. , Jeon Y. S. , Lee J.-H. , Yi H. , Won S. , Chun J. . ( 2012; ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62:, 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  17. Kimura M. . ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  18. Lal R. , Dogra C. , Malhotra S. , Sharma P. , Pal R. . ( 2006; ). Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. . Trends Biotechnol 24:, 121–130. [CrossRef] [PubMed]
    [Google Scholar]
  19. Lee J.-S. , Shin Y. K. , Yoon J.-H. , Takeuchi M. , Pyun Y.-R. , Park Y.-H. . ( 2001; ). Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. . Int J Syst Evol Microbiol 51:, 1491–1498.[PubMed]
    [Google Scholar]
  20. Lenucci M. S. , Leucci M. R. , Piro G. , Dalessandro G. . ( 2008; ). Variability in the content of soluble sugars and cell wall polysaccharides in red-ripe cherry and high-pigment tomato cultivars. . J Sci Food Agric 88:, 1837–1844. [CrossRef]
    [Google Scholar]
  21. Lobas D. , Nimtz M. , Wray V. , Schumpe A. , Proppe C. , Deckwer W. D. . ( 1994; ). Structure and physical properties of the extracellular polysaccharide PS-P4 produced by Sphingomonas paucimobilis P4 (DSM 6418). . Carbohydr Res 251:, 303–313. [CrossRef] [PubMed]
    [Google Scholar]
  22. McConaughy B. L. , Laird C. D. , McCarthy B. J. . ( 1969; ). Nucleic acid reassociation in formamide. . Biochemistry 8:, 3289–3295. [CrossRef] [PubMed]
    [Google Scholar]
  23. 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 quinines and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  24. Moss C. W. , Guerrant G. O. . ( 1983; ). Separation of bacterial ubiquinones by reverse-phase high-pressure liquid chromatography. . J Clin Microbiol 18:, 15–17.[PubMed]
    [Google Scholar]
  25. Nampoothiria K. M. , Singhania R. R. , Sabarinatha C. , Pandey A. . ( 2003; ). Fermentative production of gellan using Sphingomonas paucimobilis . . Process Biochem 38:, 1513–1519. [CrossRef]
    [Google Scholar]
  26. Nilgiriwala K. S. , Alahari A. , Rao A. S. , Apte S. K. . ( 2008; ). Cloning and overexpression of alkaline phosphatase PhoK from Sphingomonas sp. strain BSAR-1 for bioprecipitation of uranium from alkaline solutions. . Appl Environ Microbiol 74:, 5516–5523. [CrossRef] [PubMed]
    [Google Scholar]
  27. Ohta H. , Hattori R. , Ushiba Y. , Mitsui H. , Ito M. , Watanabe H. , Tonosaki A. , Hattori T. . ( 2004; ). Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. . Int J Syst Evol Microbiol 54:, 2185–2190. [CrossRef] [PubMed]
    [Google Scholar]
  28. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  29. Scherer P. , Kneifel H. . ( 1983; ). Distribution of polyamines in methanogenic bacteria. . J Bacteriol 154:, 1315–1322.[PubMed]
    [Google Scholar]
  30. Seo E. J. , Yoo S. H. , Oh K. W. , Cha J. , Lee H. G. , Park C. S. . ( 2004; ). Isolation of an exopolysaccharide-producing bacterium, Sphingomonas sp. CS101, which forms an unusual type of sphingan. . Biosci Biotechnol Biochem 68:, 1146–1148. [CrossRef] [PubMed]
    [Google Scholar]
  31. Shaw F. L. , Elliott K. A. , Kinch L. N. , Fuell C. , Phillips M. A. , Michael A. J. . ( 2010; ). Evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine. . J Biol Chem 285:, 14711–14723. [CrossRef] [PubMed]
    [Google Scholar]
  32. Sober E. . ( 1983; ). Parsimony in systematics: philosophical issues. . Annu Rev Ecol Syst 14:, 335–357. [CrossRef]
    [Google Scholar]
  33. Stabili L. , Gravili C. , Tredici S. M. , Piraino S. , Talà A. , Boero F. , Alifano P. . ( 2008; ). Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. . Microb Ecol 56:, 625–636. [CrossRef] [PubMed]
    [Google Scholar]
  34. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  35. Stolz A. . ( 2009; ). Molecular characteristics of xenobiotic-degrading sphingomonads. . Appl Microbiol Biotechnol 81:, 793–811. [CrossRef] [PubMed]
    [Google Scholar]
  36. Takeuchi M. , Hiraishi A. . ( 2001; ). Taxonomic significance of 2-hydroxy fatty acid profiles of the species in the genus Sphingomonas and related taxa. . IFO Res Commun 20:, 72–82.
    [Google Scholar]
  37. Takeuchi M. , Sakane T. , Yanagi M. , Yamasato K. , Hamana K. , Yokota A. . ( 1995; ). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.. Int J Syst Bacteriol 45:, 334–341. [CrossRef] [PubMed]
    [Google Scholar]
  38. Takeuchi M. , Hamana K. , Hiraishi A. . ( 2001; ). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. . Int J Syst Evol Microbiol 51:, 1405–1417.[PubMed]
    [Google Scholar]
  39. Thompson J. D. , Higgins D. G. , Gibson T. J. . ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22:, 4673–4680. [CrossRef] [PubMed]
    [Google Scholar]
  40. Tindall B. J. , Rosselló-Móra R. , Busse H.-J. , Ludwig W. , Kämpfer P. . ( 2010; ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60:, 249–266. [CrossRef] [PubMed]
    [Google Scholar]
  41. Vigliotta G. , Nutricati E. , Carata E. , Tredici S. M. , De Stefano M. , Pontieri P. , Massardo D. R. , Prati M. V. , De Bellis L. , Alifano P. . ( 2007; ). Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. . Appl Environ Microbiol 73:, 3556–3565. [CrossRef] [PubMed]
    [Google Scholar]
  42. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. . & other authors ( 1987; ). International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  43. West T. P. , Strohfus B. . ( 1998; ). Effect of carbon source on exopolysaccharide production by Sphingomonas paucimobilis ATCC 31461. . Microbiol Res 153:, 322–327.[CrossRef]
    [Google Scholar]
  44. White D. C. , Sutton S. D. , Ringelberg D. B. . ( 1996; ). The genus Sphingomonas: physiology and ecology. . Curr Opin Biotechnol 7:, 301–306. [CrossRef] [PubMed]
    [Google Scholar]
  45. Yabuuchi E. , Yano I. , Oyaizu H. , Hashimoto Y. , Ezaki T. , Yamamoto H. . ( 1990; ). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . . Microbiol Immunol 34:, 99–119.[PubMed] [CrossRef]
    [Google Scholar]
  46. Yoon J. H. , Kang S. J. , Lee S. Y. , Oh T. K. . ( 2008; ). Sphingomonas insulae sp. nov., isolated from soil. . Int J Syst Evol Microbiol 58:, 231–236. [CrossRef] [PubMed]
    [Google Scholar]
  47. Yoon J. H. , Park S. , Kang S. J. , Kim W. , Oh T. K. . ( 2009; ). Sphingomonas hankookensis sp. nov., isolated from wastewater. . Int J Syst Evol Microbiol 59:, 2788–2793. [CrossRef] [PubMed]
    [Google Scholar]
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