1887

Abstract

A bacterial strain, designated FSY-8, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8 were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20–40 °C (optimum, 30–37 °C) and pH 5–7 (optimum, pH 6) and in the presence of 0–0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8 were summed feature 8 (C 7 and/or C 6) and summed feature 3 (C 7 and/or C 6). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8 formed a phylogenetic lineage in the genus . Strain FSY-8 showed 71.6–77.2 % average nucleotide identity and 19.9–22.8 % digital DNA–DNA hybridization identity with the strains of other species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8 should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FSY-8 (=BCRC 81051=LMG 30053=KCTC 52812).

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2020-09-04
2021-02-26
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References

  1. 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 [CrossRef][PubMed]
    [Google Scholar]
  2. Lee L-H, Azman A-S, Zainal N, Eng S-K, Fang C-M et al. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. Int J Syst Evol Microbiol 2014; 64:1194–1201 [CrossRef][PubMed]
    [Google Scholar]
  3. Lin S-Y, Hameed A, Liu Y-C, Hsu Y-H, Lai W-A et al. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana . Int J Syst Evol Microbiol 2014; 64:594–598 [CrossRef][PubMed]
    [Google Scholar]
  4. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  5. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [CrossRef][PubMed]
    [Google Scholar]
  6. Yoon S-H, Ha S-M, 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]
  7. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  8. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  11. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [CrossRef]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  13. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [CrossRef][PubMed]
    [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  15. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  16. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  21. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef][PubMed]
    [Google Scholar]
  22. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef][PubMed]
    [Google Scholar]
  23. Beveridge TJ, Lawrence JR, Murray RGE et al. Sampling and staining for light microscopy. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 19–33
    [Google Scholar]
  24. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 1970; 71:283–294 [CrossRef][PubMed]
    [Google Scholar]
  25. Spiekermann P, Rehm BH, Kalscheuer R, Baumeister D, Steinbüchel A. A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 1999; 171:73–80 [CrossRef][PubMed]
    [Google Scholar]
  26. Breznak JA, Costilow RN et al. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 309–329
    [Google Scholar]
  27. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  28. Wen C-M, Tseng C-S, Cheng C-Y, Li Y-K. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002; 35:213–219 [CrossRef][PubMed]
    [Google Scholar]
  29. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [CrossRef][PubMed]
    [Google Scholar]
  30. Chang S-C, Wang J-T, Vandamme P, Hwang J-H, Chang P-S et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004; 27:43–49 [CrossRef][PubMed]
    [Google Scholar]
  31. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37 [CrossRef]
    [Google Scholar]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  33. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 121–161
    [Google Scholar]
  34. Sheu S-Y, Liu L-P, Chen W-M. Novosphingobium bradum sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:5083–5090 [CrossRef][PubMed]
    [Google Scholar]
  35. Kämpfer P, Witzenberger R, Denner EBM, Busse H-J, Neef A. Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst Appl Microbiol 2002; 25:37–45 [CrossRef][PubMed]
    [Google Scholar]
  36. Nguyen TM, Myung S-W, Jang H, Kim J. Description of Novosphingobium flavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:3642–3650 [CrossRef][PubMed]
    [Google Scholar]
  37. Sheu S-Y, Cai C-Y, Kwon S-W, Chen W-M. Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm. Int J Syst Evol Microbiol 2020; 70:1122–1132 [CrossRef][PubMed]
    [Google Scholar]
  38. Sheu S-Y, Chen Z-H, Chen W-M. Novosphingobium piscinae sp. nov., isolated from a fish culture pond. Int J Syst Evol Microbiol 2016; 66:1539–1545 [CrossRef][PubMed]
    [Google Scholar]
  39. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [CrossRef]
    [Google Scholar]
  40. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [CrossRef]
    [Google Scholar]
  41. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 265–309
    [Google Scholar]
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