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

Volume 71, Issue 3

sp. nov., a flavobacterium isolated from Antarctic soil Free

Abstract

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile, yellow-pigmented bacteria, designated strain G5-32, belonging to the genus was isolated from soil collected in the Antarctic. The strain was identified using a polyphasic taxonomic approach. The strain grew in the presence of 0–5% (w/v) NaCl (optimum, 1%), at pH 6.0–9.0 (optimum, pH 8.0) and at 4–28 °C (optimum, 20 °C). The predominant menaquinone was MK-6 (99.4%). The major fatty acids were anteiso-C (28.2%), iso-C (16.4%), summed feature 9 (comprising iso-C 9 and/or 10-methyl C; 10.6%) and iso-C (5.9%). A phylogenetic tree based on 16S rRNA gene sequences showed that strain G5-32 formed a lineage within the genus with the closest phylogenetic neighbours HMD1043, DSM 23145, DSM 17048 and NCTC 13525 (97.9, 97.8, 97.8 and 98.0 % 16S rRNA gene sequence similarity, respectively). The ANI values between strain G5-32 and DSM 17048, DSM 23145, NCTC 13525 and HMD1043 were 90.9, 82.6, 77.1 and 76.3%. Concurrently, digital DNA–DNA hybridization values of strain G5-32 assessed against DSM 17048, DSM 23145, NCTC 13525 and HMD1043 were 42.3, 25.9, 21.7 and 21.3%, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, sp. nov., is proposed. The type strain is G5-32 (=CCTCC AA 2019083=KCTC 72766).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antarctic soil , Flavobacteria , Kaistella gelatinilytica and polyphasic taxonomy
Funding
This study was supported by the:
  • the National Key R&D Program of China (Award 2018YFC1406705)
    • Principal Award Recipient: JingLi
© 2021 The Authors
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2021-03-16
2025-11-12

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References

  1. Vandamme P, Bernardet JF, Segers P, Kersters K, Holmes B. Notes: new perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994; 44:827–831 [View Article]
     [Google Scholar]
  2. Kämpfer P, Vaneechoutte M, Lodders N, De Baere T, Avesani V et al. Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium . Int J Syst Evol Microbiol 2009; 59:2421–2428 [View Article][PubMed]
     [Google Scholar]
  3. Yassin AF, Hupfer H, Siering C, Busse H-J. Chryseobacterium treverense sp. nov., isolated from a human clinical source. Int J Syst Evol Microbiol 2010; 60:1993–1998 [View Article][PubMed]
     [Google Scholar]
  4. Kim MK, Im W-T, Shin YK, Lim JH, Kim S-H et al. Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch. Int J Syst Evol Microbiol 2004; 54:2319–2324 [View Article][PubMed]
     [Google Scholar]
  5. Pires C, Carvalho MF, De Marco P, Magan N, Castro PML. Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol 2010; 60:402–407 [View Article][PubMed]
     [Google Scholar]
  6. Guo W, Li J, Shi M, Yuan K, Li N et al. Chryseobacterium montanum sp. nov. isolated from mountain soil. Int J Syst Evol Microbiol 2016; 66:4051–4056 [View Article][PubMed]
     [Google Scholar]
  7. Hantsis-Zacharov E, Halpern M. Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk. Int J Syst Evol Microbiol 2007; 57:2344–2348 [View Article][PubMed]
     [Google Scholar]
  8. Benmalek Y, Cayol J-L, Bouanane NA, Hacene H, Fauque G et al. Chryseobacterium solincola sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:1876–1880 [View Article][PubMed]
     [Google Scholar]
  9. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  10. Bernardet JF, Vancanneyt M, Matte-Tailliez O, Grisez L, Tailliez P et al. Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst Appl Microbiol 2005; 28:640–660 [View Article][PubMed]
     [Google Scholar]
  11. Peterson WJ, Bell TA, Etchells JL, Smart WW. A procedure for demonstrating the presence of carotenoid pigments in yeasts. J Bacteriol 1954; 67:708–713 [View Article][PubMed]
     [Google Scholar]
  12. Mccarthy AJ, Cross T. A taxonomic study of Thermomonospora and other monosporic actinomycetes. Microbiology 1984; 130:5–25 [View Article]
     [Google Scholar]
  13. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  14. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology 4 Baltimore: Williams & Wilkins; 1989 pp 2452–2492
     [Google Scholar]
  15. Xu S, Yan L, Zhang X, Wang C, Feng G et al. Nocardiopsis fildesensis sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2014; 64:174–179 [View Article][PubMed]
     [Google Scholar]
  16. Anand S, Bala K, Saxena A, Schumann P, Lal R. Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site. Int J Syst Evol Microbiol 2012; 62:2114–2120 [View Article][PubMed]
     [Google Scholar]
  17. 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]
  18. Minnikin DE, Dobson G, Draper P. Characterization of Mycobacterium leprae by lipid analysis. Acta Leprol 1984; 2:113–120[PubMed]
     [Google Scholar]
  19. 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]
  20. Sabry SA, Ghanem NB, Abu-Ella GA, Schumann P, Stackebrandt E et al. Nocardiopsis aegyptia sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2004; 54:453–456 [View Article][PubMed]
     [Google Scholar]
  21. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  22. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2001; 51:357–363 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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][PubMed]
     [Google Scholar]
  27. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019; 35:4453–4455 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. 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]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. 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][PubMed]
     [Google Scholar]
  35. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
     [Google Scholar]
  36. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  37. Stropko SJ, Pipes SE, Newman JD. Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus . Int J Syst Evol Microbiol 2014; 64:3804–3809 [View Article][PubMed]
     [Google Scholar]
  38. 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]
  39. Holmes B, Steigerwalt AG, Nicholson AC. DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. Int J Syst Evol Microbiol 2013; 63:4639–4662 [View Article][PubMed]
     [Google Scholar]
  40. Kämpfer P, Fallschissel K, Avendaño-Herrera R. Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar). Int J Syst Evol Microbiol 2011; 61:497–501 [View Article][PubMed]
     [Google Scholar]
  41. Yi H, Yoon HI, Chun J. Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic. Int J Syst Evol Microbiol 2005; 55:409–416 [View Article][PubMed]
     [Google Scholar]
  42. Joung Y, Joh K. Chryseobacterium yonginense sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2011; 61:1413–1417 [View Article][PubMed]
     [Google Scholar]
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Kaistella gelatinilytica sp. nov., a flavobacterium isolated from Antarctic soil
Int J Syst Evol Microbiol 71, 004753 (2021); https://doi.org/10.1099/ijsem.0.004753
/content/journal/ijsem/10.1099/ijsem.0.004753
/content/journal/ijsem/10.1099/ijsem.0.004753
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