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Abstract

A Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901, was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10′ 24′′ N; 112° 32′ 10′′ E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901 belongs to the genus Chitinophaga , and showed the highest similarities to Chitinophaga sancti NBRC 15057 (98.6 %) and Chitinophaga oryziterrae JCM 16595 (96.9 %). The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901 was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain K20C18050901 and C. sancti NBRC 15057 were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901 represents a novel species of the genus Chitinophaga , for which the name Chitinophaga silvisoli sp. nov. is proposed. The type strain is K20C18050901 (=GDMCC 1.1411=KCTC 62860).

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2019-01-04
2020-01-24
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References

  1. Kämpfer P, Lodders N, Falsen E. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 2011;61:518–523 [CrossRef][PubMed]
    [Google Scholar]
  2. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981;31:285–293 [CrossRef]
    [Google Scholar]
  3. Zhang L, Liao S, Tan Y, Wang G, Wang D et al. Chitinophaga barathri sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2015;65:4233–4238 [CrossRef][PubMed]
    [Google Scholar]
  4. Chung EJ, Park TS, Jeon CO, Chung YR. Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2012;62:3030–3035 [CrossRef][PubMed]
    [Google Scholar]
  5. Lv YY, Wang J, You J, Qiu LH. Chitinophaga dinghuensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015;65:4816–4822 [CrossRef][PubMed]
    [Google Scholar]
  6. Li N, Chen T, Cheng D, Xu XJ, He J. Chitinophaga sedimenti sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017;67:3485–3489 [CrossRef][PubMed]
    [Google Scholar]
  7. Jin D, Kong X, Wang J, Sun J, Yu X et al. Chitinophaga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018;68:2209–2213 [CrossRef][PubMed]
    [Google Scholar]
  8. Gao S, Zhang WB, Sheng XF, He LY, Huang Z. Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock. Int J Syst Evol Microbiol 2015;65:418–423 [CrossRef][PubMed]
    [Google Scholar]
  9. Cheng C, Wang Q, He LY, Huang Z, Sheng XF. Chitinophaga qingshengii sp. nov., isolated from weathered rock surface. Int J Syst Evol Microbiol 2015;65:280–285 [CrossRef][PubMed]
    [Google Scholar]
  10. Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO et al. Chitinophaga eiseniae sp. nov., isolated from vermicompost. Int J Syst Evol Microbiol 2011;61:2373–2378 [CrossRef][PubMed]
    [Google Scholar]
  11. Proença DN, Nobre MF, Morais PV. Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis. Int J Syst Evol Microbiol 2014;64:1237–1243 [CrossRef][PubMed]
    [Google Scholar]
  12. Ke Z, Yang MJ, Jia WB, Mu Y, Li JL et al. Chitinophaga parva sp. nov., a new member of the family Chitinophagaceae, isolated from soil in a chemical factory. Int J Syst Evol Microbiol 2018;68:3452–3457 [CrossRef][PubMed]
    [Google Scholar]
  13. Reichenbach H, Dworkin M. The myxobacteria. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes. New York: Springer 1992; pp.3416–3487
    [Google Scholar]
  14. Shimkets LJ, Dworkin M, Reichenbach H. The Myxobacteria. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) In the Prokaryotes New York: Springer; 2006; pp.31–115
    [Google Scholar]
  15. Chen D-H, Ronald PC. A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Report 1999;17:53–57 [CrossRef]
    [Google Scholar]
  16. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015;31:587–589 [CrossRef][PubMed]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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]
  19. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52:696–704 [CrossRef][PubMed]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971;20:406–416 [CrossRef]
    [Google Scholar]
  21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. Lv YY, Wang J, Chen MH, You J, Qiu LH. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016;66:1785–1791 [CrossRef][PubMed]
    [Google Scholar]
  27. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) In Methods for General and Molecular Microbiologyvol. 365 Washington, DC: American Society for Microbiology; 2007; pp.384–385
    [Google Scholar]
  30. Kämpfer P, Young CC, Sridhar KR, Arun AB, Lai WA et al. Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 2006;56:2223–2228 [CrossRef][PubMed]
    [Google Scholar]
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