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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 6

sp. nov., isolated from forest soil Free

Abstract

A novel bacterial strain, designated ysch24, was isolated from a forest soil sample collected from the Cat Tien National Park, southern Vietnam. Cells were Gram-stain-negative, aerobic, gliding, filamentous or rod-shaped. The results of 16S rRNA gene analyses revealed that strain ysch24 belongs to the genus , and was most closely related to GDMCC 1.1411 (97.4 %), followed by JCM 16595 (97.3 %) and NBRC 15057 (96.9 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain ysch24 and closely related type strains were 72.0–74.0 % and 19.1–19.4 %, respectively. Major fatty acids were iso-C, C ω5 and iso-C 3-OH and the predominant respiratory quinone was menaquinone 7. Polar lipids consisted of phosphatidylethanolamine, four unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. The genomic DNA G+C content was 45.6 mol%. The study clearly showed that strain ysch24 should represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ysch24 (=GDMCC 1.1355=KACC 21527).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ANI , Chitinophaga tropicalis , dDDH , forest soil and whole genome sequence
Funding
This study was supported by the:
  • Medical Science and Technology Foundation of Guangdong Province (CN) (Award 2019B030316010)
    • Principle Award Recipient: Xian-Jiao Zhang
  • the GDAS' Special Project of Science and Technology Development (Award 2020GDASYL-20200302002)
    • Principle Award Recipient: Hong-Hui Zhu
  • the Key Realm R&D Program of Guangdong Province (Award 2018B020205001)
    • Principle Award Recipient: Hong-Hui Zhu
© 2020 The Authors
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2020-06-05
2024-12-12
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References

  1. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981; 31:285–293 [View Article]
     [Google Scholar]
  2. Kämpfer P, Young C-C, 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 [View Article][PubMed]
     [Google Scholar]
  3. Zong Y, Wu M, Liu X, Jin Y, Wang G, Li M et al. Chitinophaga lutea sp. nov., isolated from arsenic-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2114–2119 [View Article][PubMed]
     [Google Scholar]
  4. Kong X-K, Chen D, Huang J-W, Cheng X-K, Jiang J-D. Chitinophaga deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2019; 69:1783–1788 [View Article][PubMed]
     [Google Scholar]
  5. Wang C, Lv Y, Li A, Feng G, Bao G et al. Chitinophaga silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:909–913 [View Article][PubMed]
     [Google Scholar]
  6. Zou Y, Zhang X, Song H, Liu Y, Cheng Q. Chitinophaga alhagiae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia . Int J Syst Evol Microbiol 2019; 69:1179–1184 [View Article][PubMed]
     [Google Scholar]
  7. Lv Y-Y, Wang C-L, Feng G-da, Yao Q, Su B-L et al. Chitinophaga flava sp. nov., isolated from monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2019; 69:625–630 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article][PubMed]
     [Google Scholar]
  9. Li N, Chen T, Cheng D, Xu X-J, He J. Chitinophaga sediment sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:3485–3489 [View Article][PubMed]
     [Google Scholar]
  10. Li L, Sun L, Shi N, Liu L, Guo H et al. Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots. Int J Syst Evol Microbiol 2013; 63:1800–1804 [View Article][PubMed]
     [Google Scholar]
  11. Reichenbach H, Dworkin M. The Myxobacteria. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. (editors) The Prokaryotes, 2nd ed. New York: Springer; 1992 pp 3416–3487
     [Google Scholar]
  12. 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]
  13. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 2008; 105:17994–17999 [View Article][PubMed]
     [Google Scholar]
  14. Nübel U, Garcia-Pichel F, Muyzer G. Pcr primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 1997; 63:3327–3332 [View Article][PubMed]
     [Google Scholar]
  15. 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 [View Article][PubMed]
     [Google Scholar]
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. 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 [View Article][PubMed]
     [Google Scholar]
  27. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758 [View Article][PubMed]
     [Google Scholar]
  28. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  29. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note #101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  32. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  33. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007. pp 330–393
     [Google Scholar]
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Chitinophaga tropicalis sp. nov., isolated from forest soil
Int J Syst Evol Microbiol 70, 3859 (2020); https://doi.org/10.1099/ijsem.0.004248
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