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Volume 72, Issue 9

sp. nov., isolated from water in Baiyang Lake Open Access

Abstract

A novel Gram-stain-negative, short-rod-shaped, orange-pigmented bacterial strain, designated L-1–4 w-11, was isolated from Baiyang Lake in China. The strain grew at 15–35 °C (optimum 30 °C) and pH 7–8 (optimum pH 7) in TSA medium. The predominant polar lipids of strain L-1–4 w-11 were sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and three unidentified lipids; the major cellular fatty acids were Cω6 and summed feature 8 (Cω7 and/or Cω6); and the major respiratory quinone was ubiquinone 10 (Q-10). Strain L-1–4 w-11 showed the highest 16S rRNA gene sequence similarity to JCM 15438 (98.3 %) and GDMCC 1.657 (98.0 %). The draft genome size of strain L-1–4 w-11 was 3.3 Mbp, and the G+C content was 67.8 mol%. Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain L-1–4 w-11 and GDMCC 1.657 (76.9 and 21.0 %), JCM 15438 (76.0 and 19.9 %) and CGMCC 1.12825 (72.8 and 19.6 %) were far below the thresholds for prokaryotic conspecific assignment. With the evidence from the phylogenetic, chemotaxonomic and genotypic analyses, we propose that strain L-1–4 w-11 represents a novel species with the name sp. nov. The type strain is L-1–4 w-11 (=CGMCC 1.13572=JCM 33962).

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  • Accepted:
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Keyword(s): Baiyang Lake , freshwater and Sphingomonas baiyangensis sp. nov
Funding
This study was supported by the:
  • Science and Technology Basic Resources Investigation Project (Award 2017FY100300)
    • Principle Award Recipient: JieFeng
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-09-29
2024-05-02
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References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article]
     [Google Scholar]
  2. 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. Syst Appl Microbiol 1993; 16:227–238 [View Article]
     [Google Scholar]
  3. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article] [PubMed]
     [Google Scholar]
  4. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas. Microbiol Immunol 1999; 43:339–349 [View Article]
     [Google Scholar]
  5. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I et al. Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 2002; 52:1485–1496 [View Article] [PubMed]
     [Google Scholar]
  6. Busse H-J, Denner EBM, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 2003; 53:1253–1260 [View Article] [PubMed]
     [Google Scholar]
  7. Chen H, Jogler M, Rohde M, Klenk H-P, Busse H-J et al. Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int J Syst Evol Microbiol 2012; 62:2835–2843 [View Article] [PubMed]
     [Google Scholar]
  8. Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH. Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead–zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. Int J Syst Evol Microbiol 2017; 67:2160–2165 [View Article] [PubMed]
     [Google Scholar]
  9. Liu L, Hui N, Liang L, Zhang X, Sun Q et al. Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil. Int J Syst Evol Microbiol 2019; 69:441–446 [View Article] [PubMed]
     [Google Scholar]
  10. Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica. Int J Syst Evol Microbiol 2009; 59:1179–1182 [View Article] [PubMed]
     [Google Scholar]
  11. Choi G-M, Jo JH, Kang M-S, Kim MS, Lee S-Y et al. Sphingomonas aquatica sp. nov., isolated from tap water. Int J Syst Evol Microbiol 2017; 67:845–850 [View Article] [PubMed]
     [Google Scholar]
  12. Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017; 67:2834–2841 [View Article] [PubMed]
     [Google Scholar]
  13. Xue H, Piao C-G, Wang X-Z, Lin C-L, Guo M-W et al. Sphingomonas aeria sp. nov., isolated from air. Int J Syst Evol Microbiol 2018; 68:2866–2871 [View Article] [PubMed]
     [Google Scholar]
  14. Singh P, Kim Y-J, Hoang V-A, Farh ME-A, Yang D-C. Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng. Antonie van Leeuwenhoek 2015; 108:711–720 [View Article] [PubMed]
     [Google Scholar]
  15. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146
     [Google Scholar]
  16. Xu Y, Xu X, Lan R, Xiong Y, Ye C et al. An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. PLoS One 2013; 8:e64211 [View Article] [PubMed]
     [Google Scholar]
  17. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and Nocardin Strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  18. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. Phenotypic Characterization and the Principles of Comparative Systematics Washington, DC, USA: American Society of Microbiology; 2007
     [Google Scholar]
  19. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975; 29:422–426 [View Article] [PubMed]
     [Google Scholar]
  20. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. Int J Syst Evol Microbiol 2016; 66:315–318 [View Article] [PubMed]
     [Google Scholar]
  21. Kamekura M. Lipids of extreme halophiles. In The Biology of Halophilic Bacteria 1993 pp 135–161
     [Google Scholar]
  22. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology 2007 pp 330–393
     [Google Scholar]
  23. Collins MD. Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics 1985 pp 267–287
     [Google Scholar]
  24. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
     [Google Scholar]
  25. Hu YT, Zhou PJ, Zhou YG, Liu ZH, Liu SJ. Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake. Int J Syst Evol Microbiol 2004; 54:2091–2094 [View Article] [PubMed]
     [Google Scholar]
  26. Hou Q, Bai X, Li W, Gao X, Zhang F et al. Design of primers for evaluation of lactic acid bacteria populations in complex biological samples. Front Microbiol 2018; 9:2045 [View Article] [PubMed]
     [Google Scholar]
  27. Yang Y, Zhang R, Feng J, Wang C, Chen J. Azospirillum griseum sp. nov., isolated from lakewater. Int J Syst Evol Microbiol 2019; 69:3676–3681 [View Article] [PubMed]
     [Google Scholar]
  28. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  31. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  32. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article] [PubMed]
     [Google Scholar]
  33. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  34. 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] [PubMed]
     [Google Scholar]
  35. 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]
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Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake
Int J Syst Evol Microbiol 72, 005326 (2022); https://doi.org/10.1099/ijsem.0.005326
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