1887

Abstract

A Gram-stain-negative, short ovoid- to coccus-shaped, aerobic, non-flagellated, and nonmotile strain, designated WN007, was isolated from the natural saline–alkali wetland soil. Growth occurred at 10–45 °C (optimum 33–37 °C), pH 6.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 2–4 % NaCl). Catalase- and oxidase-positive. A comparison of the 16S rRNA gene sequence of WN007 showed the highest sequence similarities to Paracoccus chinensis (97.5 %) and Paracoccus niistensis (97.4 %). The major respiratory quinone of strain WN007 was Q10 and the fatty acid profile of strain WN007 contained a predominant amount of summed feature 7 and small quantities of C10 : 0 3OH, C16 : 00 and C18 : 00. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, aminolipid and lipid. The genome revealed that the G+C content was 63.9 mol% and the DNA–DNA relatedness values between strain WN007 and the type strains of P. chinensis CGMCC 1.7655and P. niistensis KCTC 22789 were 46.9±2.3 and 42.4±1.7 %, respectively. This was also confirmed by the low average nucleotide identity values (<83.5 %) between strain WN007 and the most closely related recognized Paracoccus species. According to these results, strain WN007 represents a novel species of the genus Paracoccus , for which the name Paracoccus salipaludis sp. nov. is proposed. The type strain is WN007 (=KCTC 52851=ACCC 19972).

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2018-10-16
2024-03-29
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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. Dastager SG, Deepa CK, Li WJ, Tang SK, Pandey A. Paracoccus niistensis sp. nov., isolated from forest soil, India. Antonie van Leeuwenhoek 2011; 99:501–506 [View Article][PubMed]
    [Google Scholar]
  3. Nguyen NL, Kim YJ, Hoang VA, Tran BT, Pham HS et al. Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng. Int J Syst Evol Microbiol 2015; 65:1491–1497 [View Article][PubMed]
    [Google Scholar]
  4. Sun X, Luo P, Li M. Paracoccus angustae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:3469–3475 [View Article][PubMed]
    [Google Scholar]
  5. Pan J, Sun C, Zhang XQ, Huo YY, Zhu XF et al. Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment. Int J Syst Evol Microbiol 2014; 64:2512–2516 [View Article][PubMed]
    [Google Scholar]
  6. Li HF, Qu JH, Yang JS, Li ZJ, Yuan HL. Paracoccus chinensis sp. nov., isolated from sediment of a reservoir. Int J Syst Evol Microbiol 2009; 59:2670–2674 [View Article][PubMed]
    [Google Scholar]
  7. Park S, Yoon SY, Jung YT, Won SM, Park DS et al. Paracoccus aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:2992–2998 [View Article][PubMed]
    [Google Scholar]
  8. Kämpfer P, Aurass P, Karste S, Flieger A, Glaeser SP. Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm. Int J Syst Evol Microbiol 2016; 66:5101–5105 [View Article][PubMed]
    [Google Scholar]
  9. Lee MJ, Lee SS. Paracoccus limosus sp. nov., isolated from activated sludge in a sewage treatment plant. Int J Syst Evol Microbiol 2013; 63:1311–1316 [View Article][PubMed]
    [Google Scholar]
  10. Sun LN, Zhang J, Kwon SW, He J, Zhou SG et al. Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system. Int J Syst Evol Microbiol 2013; 63:1132–1137 [View Article][PubMed]
    [Google Scholar]
  11. Deng ZS, Zhao LF, Xu L, Kong ZY, Zhao P et al. Paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of Sphaerophysa salsula. Int J Syst Evol Microbiol 2011; 61:665–669 [View Article][PubMed]
    [Google Scholar]
  12. Zhang G, Yang Y, Yin X, Wang S. Paracoccus pacificus sp. nov., isolated from the Western Pacific Ocean. Antonie van Leeuwenhoek 2014; 106:725–731 [View Article][PubMed]
    [Google Scholar]
  13. Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH et al. Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 2008; 58:257–261 [View Article][PubMed]
    [Google Scholar]
  14. Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A et al. A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov. Int J Syst Bacteriol 1999; 49:645–651 [View Article][PubMed]
    [Google Scholar]
  15. Siller H, Rainey FA, Stackebrandt E, Winter J. Isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov. Int J Syst Bacteriol 1996; 46:1125–1130 [View Article][PubMed]
    [Google Scholar]
  16. Urakami T, Araki H, Oyanagi H, Suzuki K, Komagata K. Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide. Int J Syst Bacteriol 1990; 40:287–291 [View Article][PubMed]
    [Google Scholar]
  17. Kamlage B. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 791
    [Google Scholar]
  18. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863–864 [View Article][PubMed]
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  22. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  24. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964[PubMed]
    [Google Scholar]
  25. de Ley J. Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 1970; 101:738–754[PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  27. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P 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][PubMed]
    [Google Scholar]
  28. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. 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][PubMed]
    [Google Scholar]
  31. 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]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 2001 pp. 1–6
    [Google Scholar]
  33. 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]
  34. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS et al. Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 1991; 41:582–587 [View Article]
    [Google Scholar]
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. 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
    [Google Scholar]
  36. Kim M, Oh HS, Park SC, 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; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  37. 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]
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