1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 1

sp. nov., a novel psychrophilic bacterium isolated from Arctic soil Free

Abstract

A novel psychrophilic, light-yellow-coloured, aerobic, Gram-stain-negative, rod-shaped, non-motile bacterium, designated strain AR-3-4 was isolated from a sample of Arctic soil. Strain AR-3-4 grew at 0–25 °C, pH 6.0–9.0 and 0–1.0 % (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain AR-3-4 belonged to the genus , with nearest phylogenetic neighbour being H7 (97.5 % sequence similarity). The strain comprised phosphatidylethanolamine as the main polar lipid, MK-6 as predominant respiratory quinone, and summed feature 3 (Cω7 and/or Cω6), anteiso-C and iso-C as the major fatty acids. The average nucleotide identity and DNA–DNA hybridization values between strain AR-3-4 and closest members were below the threshold values of 95 % and 70 %, respectively. The DNA G+C content was 33.0 mol%. Based on the polyphasic taxonomic data, the novel species sp. nov. is proposed with the type strain AR-3-4 (=KEMB 9005–740=KACC 21171=NBRC 113787).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Arctic soil , Bacteroidetes , Flavobacteriaceae , Flavobacterium cellulosilyticum sp. nov. and psychrophilic
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2019R1F1A1058501)
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003707
2019-09-11
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/1/44.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003707&mimeType=html&fmt=ahah

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923 pp. 97–117
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense . Int J Syst Evol Microbiol 2013; 63:886–892 [View Article]
     [Google Scholar]
  4. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article]
     [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article]
     [Google Scholar]
  6. Bernardet J-F, Bowman JP. The genus Flavobacterium . In White WB, Parte AC. (editors) Bergey’s Manual of Systematic Bacteriology New York, Dordrecht, Heidelberg, London: Springer; 2010 pp. 112–155
     [Google Scholar]
  7. Chaudhary DK, Kim J. Flavobacterium olei sp. nov., a novel psychrotolerant bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:2211–2218 [View Article]
     [Google Scholar]
  8. Chaudhary DK, Kim D-U, Kim D, Kim J. Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil. Sci Rep 2019; 9:4134 [View Article]
     [Google Scholar]
  9. Lee SH, Kim JM, Lee JR, Park W, Jeon CO. Flavobacterium fluvii sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2010; 60:353–357 [View Article]
     [Google Scholar]
  10. Xin Y-H, Liang Z-H, Zhang D-C, Liu H-C, Zhang J-L et al. Flavobacterium tiangeerense sp. nov., a cold-living bacterium isolated from a glacier. Int J Syst Evol Microbiol 2009; 59:2773–2777 [View Article]
     [Google Scholar]
  11. Chen W-M, Chen J-C, Sheu S-Y. Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense . Int J Syst Evol Microbiol 2014; 64:3701–3708 [View Article]
     [Google Scholar]
  12. Joung Y, Kim H, Ahn T-S, Joh K. Flavobacterium yonginense sp. nov. and Flavobacterium myungsuense sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2012; 62:806–810 [View Article]
     [Google Scholar]
  13. Ren Q, Yu M, Li Y, Zhang Y, Shi X et al. Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach. Int J Syst Evol Microbiol 2018; 68:795–800 [View Article]
     [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article]
     [Google Scholar]
  15. Yoon SH, Sm H, 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
     [Google Scholar]
  16. Pruesse E, Peplies J, Glöckner FO. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article]
     [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [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
     [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [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]
     [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791
     [Google Scholar]
  23. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article]
     [Google Scholar]
  24. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  25. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
     [Google Scholar]
  26. 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]
     [Google Scholar]
  27. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article]
     [Google Scholar]
  28. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–W184 [View Article]
     [Google Scholar]
  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article]
     [Google Scholar]
  30. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program: table 1. Mol Biol Evol 2015; 32:2798–2800 [View Article]
     [Google Scholar]
  31. Yoon S-H, Ha S-Min, 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]
     [Google Scholar]
  32. 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]
     [Google Scholar]
  33. Goordial J, Raymond-Bouchard I, Zolotarov Y, de Bethencourt L, Ronholm J et al. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol 2015fiv154 [View Article]
     [Google Scholar]
  34. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  35. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  36. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. (editors) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp. 21–33
     [Google Scholar]
  37. 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
     [Google Scholar]
  38. Breznak JA, Costilow RN. Physicochemical factors in growth. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology Washinton, DC, USA: American Society of Microbiology; 2007 pp. 309–329
     [Google Scholar]
  39. 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]
  40. Gupta P, Samant K, Sahu A. Isolation of cellulose-degrading bacteria and determination of their cellulolytic potential. Int J Microbiol 2012; 2012:1–5 [View Article]
     [Google Scholar]
  41. Reichenbach H. The order Cytophagales . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes New York: Springer; 1992 pp. 3631–3675
     [Google Scholar]
  42. 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]
  43. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354
     [Google Scholar]
  44. Komagata K, Suzuki KI. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  45. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Tech Note 101. Newark: MIDI Inc;
     [Google Scholar]
  46. Chen W-M, Guo Y-P, Kwon S-W, Sheu C, Sheu S-Y. Flavobacterium stagni sp. nov., isolated from a freshwater reservoir. Int J Syst Evol Microbiol
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003707
Loading
Flavobacterium cellulosilyticum sp. nov., a novel psychrophilic bacterium isolated from Arctic soil
Int J Syst Evol Microbiol 70, 44 (2020); https://doi.org/10.1099/ijsem.0.003707
/content/journal/ijsem/10.1099/ijsem.0.003707
/content/journal/ijsem/10.1099/ijsem.0.003707
Loading

Data & Media loading...

Supplements

Supplementary File 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