1887

Abstract

An aerobic, Gram-stain-negative, rod-shaped, non-motile, mesophilic soil bacterium, strain WS5A3p, was isolated from a pesticide burial site in north-west Poland. The strain grew at 12–37 °C, at pH 8–9 and with 0–2 % (w/v) NaCl. The main fatty acids detected in WS5A3p were summed feature 3, summed feature 8 and C16 : 0. The major respiratory quinone was Q-10 and major polar lipids were phosphatidylethanolamine, sphingoglycolipid and phosphatidylglycerol. The G+C content of the genome was 65.1 mol%. Phylogenetic pairwise distance analysis of the 16S rRNA gene placed this strain within the genus Sphingopyxis , with the highest similarity to Sphingopyxis witflariensis W-50 (98.8 %), Sphingopyxis bauzanensis BZ30 and Sphingopyxis ginsengisoli Gsoil 250 (98.3 %) and Sphingopyxis granuli NBRC 100800 (98.09 %). Genomic similarity analyses using ANIb and dDDH algorithms indicated levels of similarity of 81.44, 80.84 and 81.16 % between WS5A3p and S. witflariensis , S. bauzanensis and S. granuli , respectively for average nucleotide identity and 25.90, 25.00 and 26.10 % for digital DNA–DNA hybridization. Based on the phylogenetic and phenotypic data, strain WS5A3p should be considered as a representative of a novel Sphingopyxis species. The name Sphingopyxis lindanitolerans sp. nov. is proposed with the type strain WS5A3p (=DSM 106274=PCM 2932).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003094
2018-11-05
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/12/3935.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003094&mimeType=html&fmt=ahah

References

  1. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera. Int J Syst Evol Microbiol 2001; 51:1405–1417
    [Google Scholar]
  2. Jogler M, Chen H, Simon J, Rohde M, Busse HJ et al. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int J Syst Evol Microbiol 2013; 63:1342–1349 [View Article][PubMed]
    [Google Scholar]
  3. Yang SZ, Xiong X, Feng GD, Li HP, Zhu HH. Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus. Int J Syst Evol Microbiol 2017; 67:4328–4331 [View Article][PubMed]
    [Google Scholar]
  4. Vancanneyt M, Schut F, Snauwaert C, Goris J, Swings J et al. Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int J Syst Evol Microbiol 2001; 51:73–79 [View Article][PubMed]
    [Google Scholar]
  5. Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F et al. Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:2618–2622 [View Article][PubMed]
    [Google Scholar]
  6. Godoy F, Vancanneyt M, Martínez M, Steinbüchel A, Swings J et al. Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 2003; 53:473–477 [View Article][PubMed]
    [Google Scholar]
  7. Verma H, Rani P, Kumar Singh A, Kumar R, Dwivedi V et al. Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3720–3726 [View Article][PubMed]
    [Google Scholar]
  8. Oelschlägel M, Rückert C, Kalinowski J, Schmidt G, Schlömann M et al. Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid. Int J Syst Evol Microbiol 2015; 65:3008–3015 [View Article][PubMed]
    [Google Scholar]
  9. Lee M, Ten LN, Lee HW, Oh HW, Im WT et al. Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2008; 58:2342–2347 [View Article][PubMed]
    [Google Scholar]
  10. Kim MK, Im WT, Ohta H, Lee M, Lee ST. Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria. J Microbiol 2005; 43:152–157[PubMed]
    [Google Scholar]
  11. Jindal S, Dua A, Lal R. Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite. Int J Syst Evol Microbiol 2013; 63:2186–2191 [View Article][PubMed]
    [Google Scholar]
  12. Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C. Sphingopyxis italica sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2013; 63:2565–2569 [View Article][PubMed]
    [Google Scholar]
  13. Takeuchi M, Kawai F, Shimada Y, Yokota A. Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol 1993; 16:227–238 [View Article]
    [Google Scholar]
  14. Chaudhary DK, Kim J. Sphingopyxis nepalensis sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:364–370 [View Article][PubMed]
    [Google Scholar]
  15. Lee HW, Ten IL, Jung HM, Liu QM, Im WT et al. Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. J Microbiol Biotechnol 2008; 18:1011–1015[PubMed]
    [Google Scholar]
  16. Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M et al. Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:2358–2363 [View Article][PubMed]
    [Google Scholar]
  17. Choi JH, Kim MS, Jung MJ, Roh SW, Shin KS et al. Sphingopyxis soli sp. nov., isolated from landfill soil. Int J Syst Evol Microbiol 2010; 60:1682–1686 [View Article][PubMed]
    [Google Scholar]
  18. Chaudhary DK, Dahal RH, Kim J. Sphingopyxis solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:1820–1826 [View Article][PubMed]
    [Google Scholar]
  19. Pal R, Bhasin VK, Lal R. Proposal to reclassify [Sphingomonas] xenophaga Stolz et al. 2000 and [Sphingomonas] taejonensis Lee et al. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively. Int J Syst Evol Microbiol 2006; 56:667–670 [View Article][PubMed]
    [Google Scholar]
  20. Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR et al. 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 2001; 51:1491–1498 [View Article][PubMed]
    [Google Scholar]
  21. Sharma P, Verma M, Bala K, Nigam A, Lal R. Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 2010; 60:780–784 [View Article][PubMed]
    [Google Scholar]
  22. Kämpfer P, Witzenberger R, Denner EB, Busse HJ, Neef A. Sphingopyxis witflariensis sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2002; 52:2029–2034 [View Article][PubMed]
    [Google Scholar]
  23. Cavicchioli R, Ostrowski M, Fegatella F, Goodchild A, Guixa-Boixereu N. Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis). Microb Ecol 2003; 46:249–256 [View Article]
    [Google Scholar]
  24. Battu L, Reddy MM, Goud BS, Ulaganathan K, Kandasamy U. Genome inside genome: NGS based identification and assembly of endophytic Sphingopyxis granuli and Pseudomonas aeruginosa genomes from rice genomic reads. Genomics 2017; 109:141–146 [View Article][PubMed]
    [Google Scholar]
  25. Kim J, Kim SJ, Kim SH, Kim SI, Moon YJ et al. Draft genome sequence of Sphingopyxis sp. strain MWB1, a crude-oil-degrading marine bacterium. Genome Announc 2014; 2:e01256-14 [View Article][PubMed]
    [Google Scholar]
  26. Yamatsu A, Matsumi R, Atomi H, Imanaka T. Isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, Sphingopyxis sp. PVA3. Appl Microbiol Biotechnol 2006; 72:804–811 [View Article][PubMed]
    [Google Scholar]
  27. Kaminski MA, Furmanczyk EM, Sobczak A, Dziembowski A, Lipinski L. Pseudomonas silesiensis sp. nov. strain A3T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence. Syst Appl Microbiol 2018; 41:13–22 [View Article][PubMed]
    [Google Scholar]
  28. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, NY: JohnWiley and Sons; 1991 pp. 115–175
    [Google Scholar]
  29. Yoon S, Ha S, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud : a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies; 2017; 671613–1617
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  31. 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]
  32. Kaminski MA, Furmanczyk EM, Dziembowski A, Sobczak A, Lipinski L. Draft genome sequence of the type strain Sphingopyxis witflariensis DSM 14551. Genome Announc 2017; 5:e00924-17 [View Article][PubMed]
    [Google Scholar]
  33. Kaminski MA, Furmanczyk EM, Dziembowski A, Sobczak A, Lipinski L. Draft genome sequence of the type strain Sphingopyxis bauzanensis DSM 22271. Genome Announc 2017; 5:e01014-17 [View Article][PubMed]
    [Google Scholar]
  34. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  37. Tambalo DD, del Bel KL, Bustard DE, Greenwood PR, Steedman AE et al. Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade. Microbiology 2010; 156:1673–1685 [View Article][PubMed]
    [Google Scholar]
  38. Heimbrook ME, Wang WL, Campbell G. Staining bacterial flagella easily. J Clin Microbiol 1989; 27:2612–2615[PubMed]
    [Google Scholar]
  39. 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]
  40. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  41. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  42. Magnes C, Fauland A, Gander E, Narath S, Ratzer M et al. Polyamines in biological samples: rapid and robust quantification by solid-phase extraction online-coupled to liquid chromatography-tandem mass spectrometry. J Chromatogr A 2014; 1331:44–51 [View Article][PubMed]
    [Google Scholar]
  43. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003094
Loading
/content/journal/ijsem/10.1099/ijsem.0.003094
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