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Volume 69, Issue 2

Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella Free

Abstract

A Gram-stain-negative, strictly aerobic bacterium, designated strain QZX222, was isolated from arsenic-contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QZX222 was clustered with Sphingosinicella vermicomposti YC7378 (97.0 %), Sphingosinicella xenopeptidilytica 3–2W4 (96.1 %), Sphingosinicella microcystinivorans Y2 (96.0 %) and Sphingosinicella soli KSL-125 (95.9 %). Compared to strain QZX222, Spingomonas olgophenolica JCM 12082 and Sphingobium boeckii 469 had 16S rRNA gene similarities of 96.2 and 95.9 %, respectively, but they located in other phylogenetic clusters. DNA–DNA hybridization and genomic ANI values between strain QZX222 and Sphingosinicella vermicomposti DSM 21593 (KCTC 22446) were 34.8 and 75.0 %, respectively. The genome size of strain QZX222 was 3.0 Mb including 2982 predicted genes. The strain had a DNA G+C content of 65.9 mol%. Strain QZX222 had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The major fatty acids (>10 %) of strain QZX222 were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C17 : 1 ω8c. The polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Strain QZX222 could be distinguished from other Sphingosinicella strains based on the results of phylogenetic and genomic analyses, DNA–DNA hybridization, white colour colony, hydrolysis of urea, alkaline phosphatase activity, lack of phosphatidylmonomethylethanolamine, and presence of phosphatidylcholine. Therefore, strain QZX222 represents a novel species of Sphingosinicella , for which the name Sphingosinicella humi sp. nov. is proposed. The type strain is QZX222 (=KCTC 62519=CCTCC AB 2018030).

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Keyword(s): novel species and Sphingosinicella
© 2019 IUMS
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2018-12-20
2024-04-25
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References

  1. Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T et al. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:85–89 [View Article][PubMed]
     [Google Scholar]
  2. Geueke B, Busse HJ, Fleischmann T, Kämpfer P, Kohler HP. Description of xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans. Int J Syst Evol Microbiol 2007; 57:107–113 [View Article][PubMed]
     [Google Scholar]
  3. Yoon JH, Kang SJ, Lee JS, Nam SW, Kim W et al. Sphingosinicella soli sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol 2008; 58:173–177 [View Article][PubMed]
     [Google Scholar]
  4. Yasir M, Aslam Z, Song GC, Jeon CO, Chung YR et al. Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella. Int J Syst Evol Microbiol 2010; 60:580–584
     [Google Scholar]
  5. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York: Wiley; 1995 pp. 2–11
     [Google Scholar]
  6. Fan H, Su C, Wang Y, Yao J, Zhao K et al. Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 2008; 105:529–539 [View Article][PubMed]
     [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  12. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  14. 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 [View Article][PubMed]
     [Google Scholar]
  15. Yassin AF, Galinski EA, Wohlfarth A, Jahnke K-D, Schaal KP et al. A new actinomycete species, Nocardiopsis lucentensis sp. nov. Int J Syst Bacteriol 1993; 43:266–271 [View Article]
     [Google Scholar]
  16. 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 [View Article][PubMed]
     [Google Scholar]
  17. Tarrand JJ, Gröschel DH. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982; 16:772–774[PubMed]
     [Google Scholar]
  18. Smibert RM, 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]
  19. Cowan ST, Steel KJ. Manual for the identification of medical bacteria. Q Rev Biol 1970; 17:680680
     [Google Scholar]
  20. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  21. Chen F, Shi Z, Wang G. Arenimonas metalli sp. nov., isolated from an iron mine. Int J Syst Evol Microbiol 2012; 62:1744–1749 [View Article][PubMed]
     [Google Scholar]
  22. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  23. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series No. 20) London: Academic Press; 1985 pp. 173–199
     [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  25. 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]
  26. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  27. Busse H-J, 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 [View Article]
     [Google Scholar]
  28. 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 [View Article]
     [Google Scholar]
  29. Chen H, Jogler M, Tindall BJ, Klenk HP, Rohde M et al. Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake. Int J Syst Evol Microbiol 2013; 63:1017–1023 [View Article][PubMed]
     [Google Scholar]
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Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella
Int J Syst Evol Microbiol 69, 498 (2019); https://doi.org/10.1099/ijsem.0.003186
/content/journal/ijsem/10.1099/ijsem.0.003186
/content/journal/ijsem/10.1099/ijsem.0.003186
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