1887

Abstract

A Gram-negative, aerobic, slightly yellow-pigmented bacterium, designated as SKLS-A10, was isolated from groundwater sample of the ‘Siklós’ petroleum hydrocarbon contaminated site (Hungary). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SKLS-A10 formed a distinct phyletic lineage within the genus Sphingobium . It shared the highest 16S rRNA gene homology with Sphingobium abikonense DSM 23268 (97.29 %), followed by Sphingobium lactosutens DSM 23389 (97.23 %), Sphingobium phenoxybenzoativorans KCTC 42448 (97.16 %) and Sphingobium subterraneum NBRC 109814 (96.74 %). The predominant fatty acids (>5 % of the total) are C18 : 1ω7c, C14 : 0 2-OH, C16 : 1 ω7c/iso C15 : 0 2-OH, C17 : 1ω6c and C16 : 0. The major ubiquinone is Q-10. The predominant polyamine is spermidine. The major polar lipids are sphingoglycolipid and diphosphatidylglycerol. The DNA G+C content of strain SKLS-A10 is 65.9 mol%. On the basis of evidence from this taxonomic study using a polyphasic approach, strain SKLS-A10 represents a novel species of the genus Sphingobium for which the name Sphingobium aquiterrae sp. nov. is proposed. The type strain is SKLS-A10 (=DSM 106441=NCAIM B. 02634).

Keyword(s): BTEX , groundwater and Sphingobium
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2018-07-05
2024-04-19
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References

  1. Takeuchi M, Hamana K, Hiraishi A. 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 2001; 51:1405–1417 [View Article][PubMed]
    [Google Scholar]
  2. Stolz A. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 2009; 81:793–811 [View Article][PubMed]
    [Google Scholar]
  3. Liang Q, Lloyd-Jones G. Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil. Int J Syst Evol Microbiol 2010; 60:413–416 [View Article][PubMed]
    [Google Scholar]
  4. Lloyd-Jones G, Lau PC. Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons. Appl Environ Microbiol 1997; 63:3286–3290[PubMed]
    [Google Scholar]
  5. Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T. Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 2003; 301:350–357 [View Article][PubMed]
    [Google Scholar]
  6. Önneby K, Håkansson S, Pizzul L, Stenström J. Reduced leaching of the herbicide MCPA after bioaugmentation with a formulated and stored Sphingobium sp. Biodegradation 2014; 25:291–300 [View Article][PubMed]
    [Google Scholar]
  7. Sipilä TP, Väisänen P, Paulin L, Yrjälä K. Sphingobium sp. HV3 degrades both herbicides and polyaromatic hydrocarbons using ortho- and meta-pathways with differential expression shown by RT-PCR. Biodegradation 2010; 21:771–784 [View Article][PubMed]
    [Google Scholar]
  8. Cai S, Shi C, Zhao JD, Cao Q, He J et al. Sphingobium phenoxybenzoativorans sp. nov., a 2-phenoxybenzoic-acid-degrading bacterium. Int J Syst Evol Microbiol 2015; 65:1986–1991 [View Article][PubMed]
    [Google Scholar]
  9. Kumari H, Gupta SK, Jindal S, Katoch P, Lal R. Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:2291–2296 [View Article][PubMed]
    [Google Scholar]
  10. Táncsics A, Farkas M, Szoboszlay S, Szabó I, Kukolya J et al. One-year monitoring of meta-cleavage dioxygenase gene expression and microbial community dynamics reveals the relevance of subfamily I.2.C extradiol dioxygenases in hypoxic, BTEX-contaminated groundwater. Syst Appl Microbiol 2013; 36:339–350 [View Article][PubMed]
    [Google Scholar]
  11. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article][PubMed]
    [Google Scholar]
  12. Ohad I, Danon D, Hestrin S. The use of shadow-casting technique for measurement of the width of elongated particles. J Cell Biol 1963; 17:321–326 [View Article][PubMed]
    [Google Scholar]
  13. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 2004
    [Google Scholar]
  14. Fahy A, McGenity TJ, Timmis KN, Ball AS. Heterogeneous aerobic benzene-degrading communities in oxygen-depleted groundwaters. FEMS Microbiol Ecol 2006; 58:260–270 [View Article][PubMed]
    [Google Scholar]
  15. Miller LT. A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 1982; 16:584–586
    [Google Scholar]
  16. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  17. Cashion P, Holder-Franklin MA, McCully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  20. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  21. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC, USA: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  22. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  23. Busse H-J, 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 [View Article]
    [Google Scholar]
  24. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
    [Google Scholar]
  25. Soergel DA, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. Isme J 2012; 6:1440–1444 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  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. 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][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  32. Tóth EM, Schumann P, Borsodi AK, Kéki Z, Kovács AL et al. Wohlfahrtiimonas chitiniclastica gen. nov., sp. nov., a new gammaproteobacterium isolated from Wohlfahrtia magnifica (Diptera: Sarcophagidae). Int J Syst Evol Microbiol 2008; 58:976–981 [View Article][PubMed]
    [Google Scholar]
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