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Volume 68, Issue 9

Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater Free

Abstract

A yellow pigmented and agar-pitting colony was isolated from a water sample obtained from a drainage ditch within a disused system of constructed wetlands. The strain was purified and named MCT13. This rod-shaped, Gram-negative, oxidase- and catalase-positive, aerobic, non-spore-forming, and non-motile strain formed round colonies and grew optimally at pH 7.5±0.2, at 28–30 °C on LB agar, with 0–0.5 % NaCl. The 16S rRNA gene sequence analysis placed the MCT13 isolate within the Sphingomonas (sensu stricto) cluster. The DNA G+C content was 65.3 %. The only observed ubiquinone was Q10. The major fatty acids included C17 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major polyamine was spermidine. The 16S rRNA gene phylogenetic analysis performed on the whole sequence, showed the closest relative of MCT13 to be Sphingomonas koreensis (98.52 %); however, there are several genotypic and phenotypic differences between the novel isolate and the type strain JSS26 of S. koreensis . On the basis of these results, strain MCT13 represents a novel species in the genus Sphingomonas , for which the name Sphingomonas turrisvirgatae sp. nov. is proposed. The type strain is MCT13 (=DSM 105457=BAC RE RSCIC 7).

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Keyword(s): agarase-producing , Alphaproteobacteria , new taxon and Sphingomonas turrisvirgatae
© 2018 IUMS
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2018-09-05
2024-04-18
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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][PubMed]
     [Google Scholar]
  2. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
     [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. Family I Sphingomonadaceae. In Garrity GM. (editor) Bergey's Manual of Systematic Bacteriology Baltimore, MD: The Williams & Wilkins Co; 2005 pp. 233–258
     [Google Scholar]
  5. Busse HJ, Denner EB, 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]
  6. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ 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]
  7. 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]
  8. Zobell C. Studies on marine bacteria: the cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
     [Google Scholar]
  9. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. D'Andrea MM, Ciacci N, Pilato DV, Rossolini GM, Thaller MC. Draft genome sequence of the agarase-producing Sphingomonas sp. MCT13. Front. Environ Sci 2017; 5:9
     [Google Scholar]
  13. 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 [View Article][PubMed]
     [Google Scholar]
  14. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR et al. Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 2001; 51:1491–1498 [View Article][PubMed]
     [Google Scholar]
  17. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
     [Google Scholar]
  18. Fluharty DM, Packard WL. Differentiation of Gram-positive and Gram-negative bacteria without staining. Am J Vet Clin Pathol 1967; 1:31–35
     [Google Scholar]
  19. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  20. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  21. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
     [Google Scholar]
  22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  23. Altieri I, Semeraro A, Scalise F, Calderari I, Stacchini P. European official control of food: determination of histamine in fish products by a HPLC-UV-DAD method. Food Chem 2016; 211:694–699 [View Article][PubMed]
     [Google Scholar]
  24. Hamana K, Sakamoto A, Tachiyanagi S, Terauchi E, Takeuchi M. Polyamine profiles of some members of the alpha subclass of the class Proteobacteria: polyamine analysis of twenty recently described genera. Microbiol Cult Collect 2003; 19:13–21
     [Google Scholar]
  25. Hamana K, Sato W, Gouma K, Yu J, Lno Y et al. Cellular polyamine catalogues of the five classes of the phylum Proteobacteria: distributions of homospermidine within the class Alphaproteobacteria, hydroxyputrescine within the class Betaproteobacteria, norspermidine within the class Gammaproteobacteria and spermine within the classes Deltaproteobacteria and Epsilonproteobacteria. Ann Gunma Health Sci 2006; 27:1–16
     [Google Scholar]
  26. Kim JH, Kim SH, Kim KH, Lee PC. Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. Int J Syst Evol Microbiol 2015; 65:2824–2830 [View Article][PubMed]
     [Google Scholar]
  27. Lee Y, Jeon CO. Sphingomonas frigidaeris sp. nov., isolated from an air conditioning system. Int J Syst Evol Microbiol 2017; 67:3907–3912 [View Article][PubMed]
     [Google Scholar]
  28. Vanbroekhoven K, Ryngaert A, Bastiaens L, Wattiau P, Vancanneyt M et al. Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples. Environ Microbiol 2004; 6:1123–1136 [View Article][PubMed]
     [Google Scholar]
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Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater
Int J Syst Evol Microbiol 68, 2794 (2018); https://doi.org/10.1099/ijsem.0.002896
/content/journal/ijsem/10.1099/ijsem.0.002896
/content/journal/ijsem/10.1099/ijsem.0.002896
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