1887

Abstract

A novel Gram-stain-negative, aerobic, non-motile, coccus-shaped bacterium, designated CFH 90064, was isolated from a salt lake sediment sample collected from Yuncheng city, Shanxi province, PR China. 16S rRNA gene sequence comparisons and phylogenetic analyses showed that the strain belonged to the genus Paracoccus and clustered with Paracoccus zeaxanthinifaciens R-1512 (98.2 % similarity), Paracoccus homiensis DD-R11 (97.6 % similarity) and Paracoccus fistulariae 22–5 (96.5 % similarity), respectively. Growth of strain CFH 90064 was observed at 10–37 °C, pH 6.0–9.0 and with NaCl concentrations of up to 6.0 % (w/v). Strain CFH 90064 contained Q-10 as the only isoprenoid quinone, and the major fatty acid was C18 : 1ω7c. Polar lipids of strain CFH 90064 comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified glycolipid, an unidentified aminolipid and an unidentified phospholipid. The genome of strain CFH 90008 was 3.75 Mbp with a DNA G+C content of 65.1 %. Based on the phylogenetic analyses, low average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain CFH 90064 could not be classified into any recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus halotolerans sp. nov. is proposed. The type strain is CFH 90064 (=CCTCC AB 2016131=DSM 103234).

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2018-12-20
2019-10-15
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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 [CrossRef]
    [Google Scholar]
  2. Kim BY, Weon HY, Yoo SH, Kwon SW, Cho YH et al. Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 2006;56:2387–2390 [CrossRef][PubMed]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Nakamura A. Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil. Int J Syst Evol Microbiol 2015;65:3878–3884 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. Ghosh W, Mandal S, Roy P. Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant. Syst Appl Microbiol 2006;29:396–403 [CrossRef][PubMed]
    [Google Scholar]
  7. Kämpfer P, Lai WA, Arun AB, Young CC, Rekha PD et al. Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban). Int J Syst Evol Microbiol 2012;62:2750–2756 [CrossRef][PubMed]
    [Google Scholar]
  8. Dominguez-Moñino I, Jurado V, Hermosin B, Saiz-Jimenez C. Paracoccus cavernae sp. nov., isolated from a show cave. Int J Syst Evol Microbiol 2016;66:2265–2270 [CrossRef][PubMed]
    [Google Scholar]
  9. Daneshvar MI, Hollis DG, Weyant RS, Steigerwalt AG, Whitney AM et al. Paracoccus yeeii sp. nov. (formerly CDC group EO-2), a novel bacterial species associated with human infection. J Clin Microbiol 2003;41:1289–1294 [CrossRef][PubMed]
    [Google Scholar]
  10. Mcginnis JM, Cole JA, Dickinson MC, Mingle LA, Lapierre P et al. Paracoccus yeeii sp. nov., isolated from clinical specimens of New York State patients. Int J Syst Evol Microbiol 2015;65:1877–1882
    [Google Scholar]
  11. Tang SK, Jiang Y, Zhi XY, Lou K, Wj L et al. Isolation methods of halophilic actinomycetes. Microbiology 2007;34:390–392
    [Google Scholar]
  12. Tarhriz V, Thiel V, Nematzadeh G, Hejazi MA, Imhoff JF et al. Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugöl Lake nearby Tabriz city, Iran. Antonie Van Leeuwenhoek 2013;104:1205–1215 [CrossRef][PubMed]
    [Google Scholar]
  13. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
  15. Thompson J. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997;25:4876–4882 [CrossRef]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific Tree Topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  21. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1:18 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef][PubMed]
    [Google Scholar]
  24. Buck JD, Nonstaining BJD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993
    [Google Scholar]
  25. Leifson E. Atlas of bacterial flagellation London: Academic Press; 1960
    [Google Scholar]
  26. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978;24:710–715 [CrossRef][PubMed]
    [Google Scholar]
  27. Lh X, Wj L, Liu ZH, Jiang CL. In Actinobacterial Systematic—Principle, Methods and Practice Beijing: Science Press; 2007
    [Google Scholar]
  28. Macfaddin JF. Biochemical Tests for Identification of Medical Bacteria Williams & Wilkins Co; 1976
    [Google Scholar]
  29. Smibert R, Krieg NR. 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.607–654
    [Google Scholar]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  31. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. Journal of Liquid Chromatography 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  32. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986;123:31–36[PubMed]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Bacteriol Rev 1990;36:407–477
    [Google Scholar]
  36. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  37. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  38. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013;195:413–418 [CrossRef][PubMed]
    [Google Scholar]
  39. Schlegel HG. Taxonomic study of Paracoccus denitrijicans. Int J Syst Evol Microbiol 1983;33:26–37
    [Google Scholar]
  40. Wang Y, Tang SK, Lou K, Mao PH, 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 [CrossRef][PubMed]
    [Google Scholar]
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