1887

Abstract

A novel Gram-stain-negative, strictly aerobic, non-spore-forming, motile with one polar flagellum and short rod-shaped bacterium, designated strain ZLT-5, was isolated from procymidone-contaminated soil sampled in Nanjing, Jiangsu, PR China. Growth occurred at 26–37 °C (optimum, 37 °C), at pH 6.0–9.0 (pH 7.0) and in the presence of 0–1.5 % NaCl (0.5 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain ZLT-5 belonged to the genus , with the highest sequence similarity to THG-DT81 (96.6 %), followed by DSM 21029 (96.5 %) and RP18 (96.3 %). The G+C content of strain ZLT-5 was 68.0 mol% (draft genome sequence). The average nucleotide identity value of the draft genomes between strain ZLT-5 and THG-DT81 was 75.4 %. Strain ZLT-5 contained ubiquinone-10 as the predominant isoprenoid quinone and -homospermidine as the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphoaminolipid and sphingoglycolipid. The main cellular fatty acids (>10 % of the total fatty acids) of strain ZLT-5 were Cω6, summed feature 3 (Cω7 and/or C ISO 2-OH) and summed feature 8 (Cω7 and/or Cω6). Based on phylogenetic analysis and physiological and biochemical characterization, strain ZLT-5 is described as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ZLT-5 (=CCTCC AB 2018188=KCTC 62840).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003581
2019-09-01
2019-10-21
Loading full text...

Full text loading...

References

  1. 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 [CrossRef][PubMed]
    [Google Scholar]
  2. 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 [CrossRef][PubMed]
    [Google Scholar]
  3. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I et al. Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 2002;52:1485–1496 [CrossRef][PubMed]
    [Google Scholar]
  4. Busse HJ, Denner EB, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. 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 2003;53:1253–1260 [CrossRef][PubMed]
    [Google Scholar]
  5. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ et al. Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int J Syst Evol Microbiol 2012;62:2835–2843 [CrossRef][PubMed]
    [Google Scholar]
  6. Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY et al. Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 2014;64:926–932 [CrossRef][PubMed]
    [Google Scholar]
  7. Choi GM, Jo JH, Kang MS, Kim MS, Lee SY et al. Sphingomonas aquatica sp. nov., isolated from tap water. Int J Syst Evol Microbiol 2017;67:845–850 [CrossRef][PubMed]
    [Google Scholar]
  8. Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH et al. Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta). Int J Syst Evol Microbiol 2018;68:133–140 [CrossRef][PubMed]
    [Google Scholar]
  9. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. Methods Gen Mol Microbiol 2007;3:19–33
    [Google Scholar]
  10. Zhang L, Zhou QX, Song M, Chen XL, Xu XH et al. Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory. Int J Syst Evol Microbiol 2015;65:4608–4614 [CrossRef][PubMed]
    [Google Scholar]
  11. Breznak JA, Costilow JA. Physicochemical factors in growth. Methods Gen Mol Microbiol 2007;3:309–329
    [Google Scholar]
  12. Tindall BJ. A Comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  13. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  14. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Marzluf JA, Schmidt TM, Snyder LR et al. (eds) Methods for General and Molecular Bacteriology, 3rd edn. Washington, DC: American Society of Microbiology; 2007; pp.330–393
    [Google Scholar]
  15. 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]
  16. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 1999;23:242–251 [CrossRef][PubMed]
    [Google Scholar]
  17. Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R et al. Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 2000;745:431–437 [CrossRef][PubMed]
    [Google Scholar]
  18. Lane DL. 16S/23S rRNA sequencing. In Stackebrandt ER, Goodfellow M. (eds) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991; pp.115–175
    [Google Scholar]
  19. 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]
  20. 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]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1–32 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. Tel-Zur N, Abbo S, Myslabodski D, Mizrahi Y. Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Mol Biol Report 1999;17:249–254 [CrossRef]
    [Google Scholar]
  27. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  28. 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]
  29. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014;64:316–324 [CrossRef][PubMed]
    [Google Scholar]
  30. Zhang JY, Liu XY, Liu SJ. Sphingomonas changbaiensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2010;60:790–795 [CrossRef][PubMed]
    [Google Scholar]
  31. Ko Y, Hwang WM, Kim M, Kang K, Ahn TY. Sphingomonas silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017;67:2704–2710 [CrossRef][PubMed]
    [Google Scholar]
  32. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003581
Loading
/content/journal/ijsem/10.1099/ijsem.0.003581
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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