Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 8

sp. nov., isolated from forest soil in Pyeongchang, Republic of Korea No Access

Abstract

Rod-shaped Gram-stain-negative, aerobic bacterial strains, designated PC14 and PC15, were isolated from a forest soil sample collected in Pyeongchang county, Gangwon-do, Republic of Korea. Strains PC14 and PC15 grew at 15–37 °C (optimum, 28–30 °C in tryptone soya agar and Mueller–Hinton agar), hydrolysed chitin and casein, and tolerated pH 8.5 and 2 % (w/v) NaCl. The strains were most closely related to members of the genus , namely DSM 3695 (98.4 %), Z29 (98.3 %), Gsoil 040 (97.8 %), MRP-15 (97.8 %) and JS16-4 (97.7 %). The type strain grew well on conventional commercial media in the laboratory, including tryptone soya agar, Mueller–Hinton agar, Reasoner's 2A agar, nutrient agar and Luria–Bertani agar. The major polar lipid profile comprised phosphatidylethanolamine, an unidentified aminolipid and unidentified polar lipids. The major respiratory quinone was menaquinone-7. The main fatty acids were iso-C, C ω5, C 3-OH, iso-C 3-OH and iso-C 3-OH. The DNA G+C content of the isolated strain based on the whole genome sequence was 46.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains PC14 and PC15 and the reference type strains ranged from 71.0 to 76.5 %, and from 20.3 to 20.7 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain PC15 could be differentiated phylogenetically and phenotypically from the recognized species of the genus . Therefore, strain PC15 is considered to represent a novel species, for which the name sp. nov. is proposed. The type strain is PC15 (=KACC 22893=JCM 35788).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidota , Chitinophaga nivalis , forest soil , novel species and Pyeongchang
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2022R1A2C1010877)
    • Principle Award Recipient: JaisooKim
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005981
2023-08-16
2025-01-24
Loading full text...

Full text loading...

References

  1. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Evol Bacteriol 1981; 31:285–293 [View Article]
     [Google Scholar]
  2. Kampfer 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 [View Article] [PubMed]
     [Google Scholar]
  3. Lee HG, An DS, Im WT, Liu QM, Jin DH et al. Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2007; 57:1396–1401 [View Article] [PubMed]
     [Google Scholar]
  4. Weon H-Y, Yoo S-H, Kim Y-J, Son J-A, Kim B-Y 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]
  5. Dahal RH, Chaudhary DK, Kim D-U, Kim J. Chitinophaga fulva sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Chaudhary DK, Kim J. Chitinophaga humicola sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:751–757 [View Article] [PubMed]
     [Google Scholar]
  8. Han S-I, Lee H-J, Whang K-S. Chitinophaga polysaccharea sp. nov., an exopolysaccharide-producing bacterium isolated from the rhizoplane of Dioscorea japonica. Int J Syst Evol Microbiol 2014; 64:55–59 [View Article] [PubMed]
     [Google Scholar]
  9. 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]
  10. Li N, Chen T, Cheng D, Xu X-J, He J. Chitinophaga sedimenti sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:3485–3489 [View Article] [PubMed]
     [Google Scholar]
  11. Wang Q, Cheng C, He L-Y, Huang Z, Sheng X-F. Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium. Int J Syst Evol Microbiol 2014; 64:260–265 [View Article] [PubMed]
     [Google Scholar]
  12. 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 [View Article] [PubMed]
     [Google Scholar]
  13. 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 [View Article] [PubMed]
     [Google Scholar]
  14. Kämpfer P. Genus I. Chitinophaga Sangkhobol and Skerman 1981, 285VP emend. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. Springer; 2009 pp 351–356
     [Google Scholar]
  15. Pham VHT, Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol 2012; 30:475–484 [View Article] [PubMed]
     [Google Scholar]
  16. Tindall BJ, Garrity GM. Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 2008; 58:1987–1990 [View Article] [PubMed]
     [Google Scholar]
  17. Cheng H-R, Jiang N. Extremely rapid extraction of DNA from bacteria and yeasts. Biotechnol Lett 2006; 28:55–59 [View Article] [PubMed]
     [Google Scholar]
  18. Moreno C, Romero J, Espejo RT. Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio. Microbiology 2002; 148:1233–1239 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. 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]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  28. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  29. Lanyi B. Classical and rapid identification method for medically important bacteria. In Cowell R. ed Methods in Microbiology Academic Press; 1987 pp 1–65
     [Google Scholar]
  30. Moyes RB, Reynolds J, Breakwell DP. Differential staining of bacteria: gram stain. Curr Protoc Microbiol 20091–8 [View Article] [PubMed]
     [Google Scholar]
  31. Krieg NR, Padgett PJ. Phenotype and physiological characterization method. In Rainey F. ed Methods in Microbiology Academic Press; 2011 pp 15–60
     [Google Scholar]
  32. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA. ed Methods for General and Molecular Microbiology ASM Press; 2007 pp 330–393 [View Article]
     [Google Scholar]
  33. Sierra G. A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 1957; 23:15–22 [View Article] [PubMed]
     [Google Scholar]
  34. Kuddus SM, Ahmad RIZ. Isolation of novel chitinolytic bacteria and production optimization of extracellular chitinase. J Gen Engg Biotechnol 2013; 11:39–46 [View Article]
     [Google Scholar]
  35. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975; 29:422–426 [View Article] [PubMed]
     [Google Scholar]
  36. 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 [View Article]
     [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In Tech Note vol 101 2001 pp 1–6
     [Google Scholar]
  38. Yao Y, Zhong X, Li H, Fan W, Xiang Q et al. Chitinophaga silvatica sp. nov., isolated from forest soil, and reclassification of Chitinophaga extrema as a later heterotypic synonym of Chitinophaga solisilvae. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  39. He SW, Ma R, Zhao YY, An L, Huang JH et al. Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea. Int J Syst Evol Microbiol 2022; 72:5335
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005981
Loading
Chitinophaga nivalis sp. nov., isolated from forest soil in Pyeongchang, Republic of Korea
Int J Syst Evol Microbiol 73, 005981 (2023); https://doi.org/10.1099/ijsem.0.005981
/content/journal/ijsem/10.1099/ijsem.0.005981
/content/journal/ijsem/10.1099/ijsem.0.005981
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error