1887

Abstract

A Gram-stain-negative, non-motile and ovoid bacterial strain, designated 4-2, was isolated from oil-contaminated water which was collected from Xinjiang Province, north-west PR China. The 16S rRNA gene sequence analysis showed that strain 4-2 belonged to the genus . The species with highest similarity to strain 4-2 was YIM 90738 (97.83 %), followed by ‘’ M26 (97.83 %) and SYSUP0003 (97.25 %). The average nucleotide identity values between 4-2 and three type strains were 84.69, 77.88 and 74.07 %, respectively. The genomic DNA G+C content of strain 4-2 was 61.4 mol%. Chemotaxonomical characteristic results showed that the respiratory quinone was ubiquinone Q-10 and the major fatty acids were summed feature 8 (C 7 or C 6) and C cyclo 8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid and an unidentified polar lipid. The predominant polyamines were putrescine, cadaverine and spermidine. On the basis of phenotypic, chemotaxonomic and phylogenetic inferences, strain 4-2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 4-2 (=CGMCC 1.13669=LMG 30882).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award Grant No. 41977198)
  • the sub-project of National Science and Technology Major Project (Award 2016ZX05040-002)
    • Principle Award Recipient: Lei Wang
  • Methodological research and application of oil field ecological profit and loss assessment (Award 2016E-1205)
    • Principle Award Recipient: Lei Wang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004036
2020-02-10
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2312.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004036&mimeType=html&fmt=ahah

References

  1. Davis DH, Doudoroff M, Stanier RY, Mandel M. Proposal to reject the genus Hydrogenomonas: Taxonomic implications. Int J Syst Bacteriol 1969; 19:375–390 [View Article]
    [Google Scholar]
  2. Ludwig W, Mittenhuber G, Friedrich CG. Transfer of Thiosphaera pantotropha to Paracoccus denitrificans . Int J Syst Bacteriol 1993; 43:363–367 [View Article]
    [Google Scholar]
  3. Katayama Y, Hiraishi A, Kuraishi H. Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus. Microbiology 1995; 141:1469–1477 [View Article]
    [Google Scholar]
  4. Meng X-L, Ming H, Huang J-R, Zhang L-Y, Cheng L-J et al. Paracoccus halotolerans sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2019; 69:523–528 [View Article]
    [Google Scholar]
  5. Ming H, Cheng L-J, Ding C-L, Niu M-M, Zhao Z-L et al. Paracoccus luteus sp. nov., isolated from the intestine of grass carp. Int J Syst Evol Microbiol 2019; 41: [View Article]
    [Google Scholar]
  6. Li J, Lu S, Jin D, Yang J, Lai X-H et al. Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2019; 49: [View Article]
    [Google Scholar]
  7. Watkinson RJ, Morgan P. Physiology of aliphatic hydrocarbon-degrading microorganisms. Biodegradation 1990; 1:79–92 [View Article]
    [Google Scholar]
  8. Cui XL, Xu LH, Zeng M, Li WJ, Mao PH et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2001; 51:357–363 [View Article]
    [Google Scholar]
  9. Yoon S-H, Ha S-M, 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 [View Article]
    [Google Scholar]
  10. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article]
    [Google Scholar]
  11. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article]
    [Google Scholar]
  12. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article]
    [Google Scholar]
  13. Jiménez G, Urdiain M, Cifuentes A, López-López A, Blanch AR et al. Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol 2013; 36:383–391 [View Article]
    [Google Scholar]
  14. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  15. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article]
    [Google Scholar]
  16. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  17. Lee M, Woo S-G, Park G, Kim MK. Paracoccus caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 2011; 61:1968–1972 [View Article]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  19. Saitou NM, Nei M. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees; 1987189–204
  20. Rzhetsky A, Nei M. Theoretical Foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  22. Leifson E. Atlas of bacterial flagellation. Am J Med Sci 1961; 242:267 [View Article]
    [Google Scholar]
  23. Xu P 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]
    [Google Scholar]
  24. Sasser M, Kunitsky C, Jackoway G, Ezzell JW, Teska JD et al. Identification of Bacillus anthracis from culture using gas chromatographic analysis of fatty acid methyl esters. J AOAC Int 2005; 88:178–181
    [Google Scholar]
  25. Collins MD, Jonse D, Goodfellow M, Minnikin DE. Isoprenoid quinone composition as a guide to the classification of Listeria, Brochothrix, Erysipelothrix and Caryophanon . J Gen Microbiol 1979; 111:453–457 [View Article]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  27. Ducros V, Ruffieux D, Belva-Besnet H, Fraipont Fde, Berger F et al. Determination of dansylated polyamines in red blood cells by liquid chromatography–tandem mass spectrometry. Anal Biochem 2009; 390:46–51 [View Article]
    [Google Scholar]
  28. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article]
    [Google Scholar]
  29. Hamana K, Matsuzaki S. Polyamines as a chemotaxonomic marker in bacterial Systematics. Crit Rev Microbiol 1992; 18:261–283 [View Article]
    [Google Scholar]
  30. Wang Y, Tang S-K, Lou K, Mao P-H, Jin X et al. Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil. Int J Syst Evol Microbiol 2009; 59:1924–1928
    [Google Scholar]
  31. Liu Y, Xie Q-yi, Hong K, Li L, Zhao Y-mei, Zhao YMetal et al. Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract. Antonie Van Leeuwenhoek 2013; 103:1133–1139
    [Google Scholar]
  32. Zhang H, Li Y-Q, Xiao M, Fang B-Z, Alkhalifah DHM et al. Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol 2019; 69:261–265
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004036
Loading
/content/journal/ijsem/10.1099/ijsem.0.004036
Loading

Data & Media loading...

Supplements

Supplementary material 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