1887

Abstract

A novel Gram-stain-negative, flagellated, rod-shaped, yellow-pigmented aerobic bacterium, strain SA925, that is capable of degrading 1-methylphenanthrene was isolated from oil-polluted soil collected from a refinery located in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain SA925 belongs to the genus and is evolutionarily close to the type strains of (98.5 % similarity), (98.2 %), (98.0 %) and (96.5 %). The G+C content of the genomic DNA was 60.2 mol%. DNA–DNA hybridization experiments between strain SA925 and the closest strain, JM-1396, revealed a low level of relatedness (35.5 %). Strain SA925 grew at 10–35 °C, at pH 6.0–8.0 and in the presence of 0–4 % (w/v) NaCl. The major fatty acids were C 7, C and summed feature 3 (C 7 and/or C 6). The polar lipid profiles mainly consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylethanolamine and sphingoglycolipid (the characteristic polar lipid). The predominant ubiquinone was Q-10. The major polyamine was spermidine. Based on the phylogenetic, phenotypic and physiological characteristics, strain SA925 was considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SA925 (=DSM 32207=GDMCC 1.1110).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001669
2017-02-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/2/489.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001669&mimeType=html&fmt=ahah

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. Kämpfer P, Witzenberger R, Denner EB, Busse HJ, Neef A. Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst Appl Microbiol 2002; 25:37–45 [View Article][PubMed]
    [Google Scholar]
  3. Fujii K, Satomi M, Morita N, Motomura T, Tanaka T et al. Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 2003; 53:47–52 [View Article][PubMed]
    [Google Scholar]
  4. Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 2004; 54:1483–1487 [View Article][PubMed]
    [Google Scholar]
  5. Kämpfer P, Martin K, Mcinroy JA, Glaeser SP. Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum. Int J Syst Evol Microbiol 2015; 65:2831–2837 [View Article][PubMed]
    [Google Scholar]
  6. Balkwill DL, Drake GR, Reeves RH, Fredrickson JK, White DC et al. Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bacteriol 1997; 47:191–201 [View Article][PubMed]
    [Google Scholar]
  7. Gao SM, Zhang YJ, Jiang N, Luo LX, Li QX et al. Novosphingobium fluoreni sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2015; 65:1409–1414 [View Article][PubMed]
    [Google Scholar]
  8. Yuan J, Lai Q, Zheng T, Shao Z. Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol 2009; 59:2084–2088 [View Article][PubMed]
    [Google Scholar]
  9. Suzuki S, Hiraishi A. Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 2007; 53:221–228 [View Article][PubMed]
    [Google Scholar]
  10. Liu ZP, Wang BJ, Liu YH, Liu SJ. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 2005; 55:1229–1232 [View Article][PubMed]
    [Google Scholar]
  11. Chen Q, Zhang J, Wang CH, Jiang J, Kwon SW et al. Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2014; 64:2573–2578 [View Article][PubMed]
    [Google Scholar]
  12. Saxena A, Anand S, Dua A, Sangwan N, Khan F et al. Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int J Syst Evol Microbiol 2013; 63:2160–2167 [View Article][PubMed]
    [Google Scholar]
  13. Lee JC, Kim SG, Whang KS. Novosphingobium aquiterrae sp. nov., isolated from ground water. Int J Syst Evol Microbiol 2014; 64:3282–3287 [View Article][PubMed]
    [Google Scholar]
  14. Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA et al. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2014; 64:594–598 [View Article][PubMed]
    [Google Scholar]
  15. Sheu SY, Liu LP, Chen WM. Novosphingobium bradum sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:5083–5090 [View Article][PubMed]
    [Google Scholar]
  16. Chen WM, Chen JC, Huang CW, Young CC, Sheu SY. Novosphingobium colocasiae sp. nov., isolated from a taro field. Int J Syst Evol Microbiol 2016; 66:673–679 [View Article][PubMed]
    [Google Scholar]
  17. Nguyen TM, Myung SW, Jang H, Kim J. Description of Novosphingobium flavum sp. nov., isolated from soil. Int J Syst Evol Micr 2016; 66:3642–3650 [CrossRef]
    [Google Scholar]
  18. Xie F, Quan S, Liu D, He W, Wang Y et al. Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. Int J Syst Evol Microbiol 2014; 64:2324–2329 [View Article][PubMed]
    [Google Scholar]
  19. Ngo HT, Trinh H, Kim JH, Yang JE, Won KH et al. Novosphingobium lotistagni sp. nov., isolated from a lotus pond. Int J Syst Evol Micr 2016; 66:4729–4734 [CrossRef]
    [Google Scholar]
  20. Lee LH, Azman AS, Zainal N, Eng SK, Fang CM et al. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. Int J Syst Evol Microbiol 2014; 64:1194–1201 [View Article][PubMed]
    [Google Scholar]
  21. Huo YY, You H, Li ZY, Wang CS, Xu XW. Novosphingobium marinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:676–680 [View Article][PubMed]
    [Google Scholar]
  22. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3170–3176 [View Article]
    [Google Scholar]
  23. Zhang L, Gao JS, Kim SG, Zhang CW, Jiang JQ et al. Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots. Int J Syst Evol Microbiol 2016; 66:302–307 [View Article][PubMed]
    [Google Scholar]
  24. Sheu SY, Chen ZH, Chen WM. Novosphingobium piscinae sp. nov., isolated from a fish culture pond. Int J Syst Evol Microbiol 2016; 66:1539–1545 [View Article][PubMed]
    [Google Scholar]
  25. Kämpfer P, Martin K, Mcinroy JA, Glaeser SP. Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere. Int J Syst Evol Microbiol 2015; 65:195–200 [View Article][PubMed]
    [Google Scholar]
  26. Chen N, Yu XJ, Yang JS, Wang ET, Li BZ et al. Novosphingobium tardum sp. nov., isolated from sediment of a freshwater lake. Antonie Van Leeuwenhoek 2015; 108:51–57 [View Article][PubMed]
    [Google Scholar]
  27. Yuan K, Wang X, Lin L, Zou S, Li Y et al. Characterizing the parent and alkyl polycyclic aromatic hydrocarbons in the Pearl River Estuary, Daya Bay and northern South China Sea: influence of riverine input. Environ Pollut 2015; 199:66–72 [View Article][PubMed]
    [Google Scholar]
  28. Zakaria MP, Takada H, Tsutsumi S, Ohno K, Yamada J et al. Distribution of polycyclic aromatic hydrocarbons (PAHs) in rivers and estuaries in Malaysia: a widespread input of petrogenic PAHs. Environ Sci Technol 2002; 36:1907–1918 [View Article][PubMed]
    [Google Scholar]
  29. Lamberts RF, Christensen JH, Mayer P, Andersen O, Johnsen AR. Isomer-specific biodegradation of methylphenanthrenes by soil bacteria. Environ Sci Technol 2008; 42:4790–4796 [View Article][PubMed]
    [Google Scholar]
  30. Sabaté J, Grifoll M, Viñas M, Solanas AM. Isolation and characterization of a 2-methylphenanthrene utilizing bacterium: identification of ring cleavage metabolites. Appl Microbiol Biotechnol 1999; 52:704–712 [View Article]
    [Google Scholar]
  31. Gilewicz M, Ni'matuzahroh, Nadalig T, Budzinski H, Doumenq P et al. Isolation and characterization of a marine bacterium capable of utilizing 2-methylphenanthrene. Appl Microbiol Biotechnol 1997; 48:528–533 [View Article][PubMed]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
  33. Yoon SH, Sm H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017 in press
    [Google Scholar]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. 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][PubMed]
    [Google Scholar]
  37. 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]
  38. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  39. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 1978; 75:4801–4805 [View Article][PubMed]
    [Google Scholar]
  40. Glaeser SP, Kämpfer P, Busse HJ, Langer S, Glaeser J. Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. Int J Syst Evol Microbiol 2009; 59:323–330 [View Article][PubMed]
    [Google Scholar]
  41. Addison SL, Foote SM, Reid NM, Lloyd-Jones G. Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. Int J Syst Evol Microbiol 2007; 57:2467–2471 [View Article][PubMed]
    [Google Scholar]
  42. Niharika N, Moskalikova H, Kaur J, Sedlackova M, Hampl A et al. Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2013; 63:667–672 [View Article][PubMed]
    [Google Scholar]
  43. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  44. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
    [Google Scholar]
  45. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:1825 [View Article]
    [Google Scholar]
  46. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  47. Wayne LG, Brenner DJ, Colwell RR. 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]
  48. 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]
  49. Cerny G. Studies on the aminopeptidase test for the distinction of gram-negative from gram-positive bacteria. Eur J Appl Microbiol 1978; 5:113–122 [View Article]
    [Google Scholar]
  50. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  51. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed]
    [Google Scholar]
  52. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496[PubMed]
    [Google Scholar]
  53. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and Related Taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
    [Google Scholar]
  54. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  55. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  56. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  57. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322[PubMed]
    [Google Scholar]
  58. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. 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 1990; 34:99–119 [View Article][PubMed]
    [Google Scholar]
  59. Gupta SK, Lal D, Lal R. Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:156–161 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001669
Loading
/content/journal/ijsem/10.1099/ijsem.0.001669
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error