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Abstract

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated H-1, was isolated from the interfacial sediment of Taihu Lake in China and characterized by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was most closely related to Rufibacter immobilis MCC P1 and Rufibacter tibetensis 1351, with sequence similarities of 98.0 and 97.6 %, respectively. DNA–DNA relatedness between strain H-1 and R. immobilis MCC P1 and R. tibetensis 1351 was 48.8 and 36.6 %, respectively. The major (>5 %) cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and anteiso-C15 : 0. The polar lipids comprised phosphatidylethanolamine, three unidentified aminophospholipids, an unidentified phospholipid and three unidentified lipids. The major respiratory quinone was menaquinone 7 (MK-7). Genomic DNA G+C content was 49.0 mol%. Based on its physiological, biochemical and chemotaxonomic characteristics, the strain represents a novel species of the genus Rufibacter , for which the name Rufibacter sediminis sp. nov. (type strain H-1=CGMCC 1.16289=NBRC 113030) is proposed.

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2019-01-23
2019-12-14
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References

  1. Abaydulla G, Luo X, Shi J, Peng F, Liu M et al. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2012;101:725–731 [CrossRef][PubMed]
    [Google Scholar]
  2. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016;39:281–296 [CrossRef][PubMed]
    [Google Scholar]
  3. Zhang ZD, Gu MY, Zhu J, Li SH, Zhang LJ et al. Rufibacter roseus sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 2015;65:1572–1577 [CrossRef][PubMed]
    [Google Scholar]
  4. Polkade AV, Ramana VV, Joshi A, Pardesi L, Shouche YS. Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake. Int J Syst Evol Microbiol 2015;65:1592–1597 [CrossRef][PubMed]
    [Google Scholar]
  5. Kýrová K, Sedláček I, Pantůček R, Králová S, Holochová P et al. Rufibacter ruber sp. nov., isolated from fragmentary rock. Int J Syst Evol Microbiol 2016;66:4401–4405 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Felföldi T, Mentes A, Schumann P, Kéki Z, Máthé I et al. Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate. Int J Syst Evol Microbiol 2016;66:5150–5154 [CrossRef][PubMed]
    [Google Scholar]
  8. Guo L. Doing battle with the green monster of Taihu Lake. Science 2007;317:1166 [CrossRef][PubMed]
    [Google Scholar]
  9. Liu ZP, Wang BJ, Liu YH, Liu SJ. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 2005;55:1229–1232 [CrossRef][PubMed]
    [Google Scholar]
  10. Cai H, Wang Y, Xu H, Yan Z, Jia B et al. Niveispirillum cyanobacteriorum sp. nov., a nitrogen-fixing bacterium isolated from cyanobacterial aggregates in a eutrophic lake. Int J Syst Evol Microbiol 2015;65:2537–2541 [CrossRef][PubMed]
    [Google Scholar]
  11. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49:1–7[PubMed]
    [Google Scholar]
  12. Gregersen T. Rapid method for distinction of Gram-negative from gram-positive bacteria. European J Applied Microbiol and Biotechnol 1978;5:123–127 [CrossRef]
    [Google Scholar]
  13. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703–704 [CrossRef][PubMed]
    [Google Scholar]
  14. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Woods WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  15. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  16. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  17. Boontosaeng T, Nimrat S, Vuthiphandchai V. Pigments production of bacteria isolated from dried seafood and capability to inhibit microbial pathogens. IOSR-JESTFT 2016;10:30–34
    [Google Scholar]
  18. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–IN1 [CrossRef]
    [Google Scholar]
  19. Johnson JL. Determination of DNA base composition. Methods Microbiol 1985;18:1–31
    [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991; pp.115–175
    [Google Scholar]
  21. 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]
  22. 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]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  24. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989;39:224–229 [CrossRef]
    [Google Scholar]
  27. 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]
  28. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962;5:109–118 [CrossRef][PubMed]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Midi Technical Note 101. Newark, De: Midi Inc; 1990
    [Google Scholar]
  30. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1987;19:161–207
    [Google Scholar]
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