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Chitinophaga parva sp. nov., a new member of the family Chitinophagaceae, isolated from soil in a chemical factory

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Chitinophaga parva sp. nov., a new member of the family Chitinophagaceae, isolated from soil in a chemical factory, Page 1 of 1

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  • A Gram-stain-negative bacterium, designated LY-1, was isolated from the soil sample collected from a chemical factory in Fuyang city, Anhui province, China. Cells of strain LY-1 were strictly aerobic, non-motile and rod-shaped. Strain LY-1 grew optimally at pH 7.0 and at 30–35 °C. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LY-1 was a member of the genus Chitinophaga and showed the highest sequence similarity to Chitinophaga costaii A37T2 (97.5 %) and lower (<97.0 %) sequence similarity to other known Chitinophaga species. Chemotaxonomic analysis revealed that strain LY-1 possessed menaquinone-7 as the major isoprenoid quinone; and iso-C15 : 0 (46.4 %), C16 : 1ω5c (27.8 %) and iso-C17 : 0 3-OH (9.0 %) were the predominant fatty acids. The polar lipids of strain LY-1 consisted of phosphatidylethanolamine, three unidentified phosphoaminolipids, one unidentified phospholipid, four unidentified lipids, two unidentified aminolipids and two unidentified glycolipids. The genomic DNA G+C content of strain LY-1 was 52.4 mol% based on total genome calculations. The average nucleotide identity and the digital DNA–DNA hybridization value of the draft genomes between strain LY-1 and strain A37T2 were 76.8 and 19.8 %, respectively. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data, and DNA–DNA hybridization, strain LY-1 is considered a novel species of the genus Chitinophaga , for which the name Chitinophaga parva sp. nov. (type strain LY-1=CCTCC AB 2018018=KCTC 62444) is proposed.

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Chitinophaga parva LY-1 is MG871256. The GenBank/EMBL/DDBJ accession numbers for the draft genome sequences of Chitinophaga parva LY-1 and Chitinophaga costaii A37T2 are QCYK00000000 and QCYL00000000, respectively.

  • Four supplementary figures are available with the online version of this article.

© 2018 IUMS | Published by the Microbiology Society

  • 1. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981;31:285–293 [CrossRef]
     [Google Scholar]
  • 2. 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]
  • 3. Lv YY, Zhang XJ, Li AZ, Zou WL, Feng GD et al. Chitinophaga varians sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2018;68: [CrossRef][PubMed]
     [Google Scholar]
  • 4. Dahal RH, Kim J. Chitinophaga caseinilytica sp. nov., a casein hydrolysing bacterium isolated from forest soil. Arch Microbiol 2018;200:645–651 [CrossRef][PubMed]
     [Google Scholar]
  • 5. 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]
  • 6. 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]
  • 7. Smibert RM, Krieg NR. Phenotypic characterization. In methods for general and molecular bacteriology 1994
     [Google Scholar]
  • 8. Bernardet JF, Nakagawa Y, Holmes B.Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049 [CrossRef][PubMed]
     [Google Scholar]
  • 9. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics. American Society of Microbiology 2007
     [Google Scholar]
  • 10. Morais PV, Francisco R, Branco R, Chung AP, da Costa MS. Leucobacter chromiireducens sp. nov., and Leucobacter aridicollis sp. nov., two new species isolated from a chromium contaminated environment. Syst Appl Microbiol 2004;27:646–652 [CrossRef][PubMed]
     [Google Scholar]
  • 11. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991;125–175
     [Google Scholar]
  • 12. Baker GC, Smith JJ, Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003;55:541–555 [CrossRef][PubMed]
     [Google Scholar]
  • 13. 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]
  • 14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
     [Google Scholar]
  • 15. 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]
  • 16. 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]
  • 17. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
     [Google Scholar]
  • 18. 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]
  • 19. Weon HY, Yoo SH, Kim YJ, Son JA, Kim BY et al. Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009;59:1267–1271 [CrossRef][PubMed]
     [Google Scholar]
  • 20. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42:989–1005 [CrossRef]
     [Google Scholar]
  • 21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. 2001
     [Google Scholar]
  • 22. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology Technical 1985
     [Google Scholar]
  • 23. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:3:199–202 [CrossRef]
     [Google Scholar]
  • 24. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
     [Google Scholar]
  • 25. Marmur J. A procedure for the isolation of deoxyribonucleic acid from microorganisms. Journal of Molecular Biology 1981;3218:208IN201
     [Google Scholar]
  • 26. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef][PubMed]
     [Google Scholar]
  • 27. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
     [Google Scholar]
  • 28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:14:60 [CrossRef][PubMed]
     [Google Scholar]
  • 29. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
     [Google Scholar]
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/content/journal/ijsem/10.1099/ijsem.0.003006
2018-09-12
2019-07-16
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