Chitinophaga deserti sp. nov., isolated from desert soil Free

Abstract

An aerobic bacterial strain, designated XJ-2, was isolated from a soil sample collected from Gurbantunggut Sandy Desert in PR China. Cells of strain XJ-2 were Gram-stain-negative, non-motile, rod-shaped and non-spore-forming. The new isolate grew well at 10–37 °C (optimum, 28–30 °C), pH 6.0–11.0 (pH 7.0) and 0–1 % (w/v) NaCl (0 %). The 16S rRNA gene sequence of strain XJ-2 showed the highest similarity to that of Chitinophaga rhizosphaerae T16R-86 (99.0 %), followed by Chitinophaga barathri YLT18 (97.0 %), Chitinophaga humicola Ktm-2 (96.7 %) and Chitinophaga niabensis JS13-10 (96.4 %). The major menaquinone of strain XJ-2 was menaquinone 7 and the predominant fatty acids (>5 %) were iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH. The polar lipids consisted of phosphatidylethanolamine, an unidentified glycolipid, three unidentified aminolipids and five unidentified lipids. The genome size was 6.33 Mb, comprising 5268 predicted genes with a G+C content of 41.5 mol%. The DNA G+C content was 50.5 mol% based on total genome calculations. The average nucleotide identity and the digital DNA–DNA hybridization values between strain XJ-2 and strain T16R-86 were 79.6 and 22.3 %, respectively. DNA–DNA relatedness between strain XJ-2 and strain YLT18 was 17.0 %. Based on the physiological, biochemical and chemotaxonomic characteristics, strain XJ-2 represents a novel species of the genus Chitinophaga , for which the name Chitinophaga deserti sp. nov. is proposed. The type strain is XJ-2 (KCTC 62443=CCTCC AB 2018019).

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2019-04-11
2024-03-29
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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 [View Article][PubMed]
    [Google Scholar]
  2. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981; 31:285–293 [View Article]
    [Google Scholar]
  3. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  4. Beveridge TJ, Lawrence JR, Murray RGE. et al. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder RL. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007
    [Google Scholar]
  5. Suzuki M, Nakagawa Y, Harayama S, Yamamoto S. Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 2001; 51:1639–1652 [View Article][PubMed]
    [Google Scholar]
  6. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  7. Gerhardt P. Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994
    [Google Scholar]
  8. Zhang H, Cheng MG, Sun B, Guo SH, Song M et al. Flavobacterium suzhouense sp. nov., isolated from farmland river sludge. Int J Syst Evol Microbiol 2015; 65:370–374 [View Article][PubMed]
    [Google Scholar]
  9. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  10. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  11. Chen F, Shi Z, Wang G. Arenimonas metalli sp. nov., isolated from an iron mine. Int J Syst Evol Microbiol 2012; 62:1744–1749 [View Article][PubMed]
    [Google Scholar]
  12. Mardis E, McCombie WR. Library quantification: fluorometric quantitation of double-stranded or single-stranded DNA samples using the qubit system. Cold Spring Harb Protoc 2017 [View Article][PubMed]
    [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt ER, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp. 115–175
    [Google Scholar]
  14. 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 [View Article]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 1870; 2016:33
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
    [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note. vol. 101 2001
    [Google Scholar]
  26. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][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 [View Article][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; 14:60 [View Article][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 [View Article]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. 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]
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