1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 7

sp. nov. and sp. nov., isolated from soil No Access

Abstract

Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4 and GMJ5, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4 and GMJ5 were both positive for catalase and oxidase. Strain PBS4-4 grew at 15–37 °C and pH 5.0–12.0. Strain GMJ5 grew at 15–37 °C and pH 5.0–11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4 and GMJ5 form a closely related cluster with the genus . The average nucleotide identity and digital DNA–DNA hybridization values between strain PBS4-4 and its closely related strains were 79.4–84.5% and 23.2–28.7 %, respectively. For GMJ5, the values were 78.3–79.3% and 22.0–22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C and summed feature 3 (C 7/C 6). Strain GMJ5 had one other major fatty acid: iso-C 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4 and GMJ5 represent novel species within the genus , and the names sp. nov. and sp. nov. are proposed, respectively. The type strain of is PBS4-4 (=KACC 22882=TBRC 17052) and the type strain of is GMJ5 (=KACC 22883=TBRC 17053).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Chryseobacterium , novel species and phylogenetic analysis
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005989
2023-07-25
2024-05-09
Loading full text...

Full text loading...

References

  1. Vandamme P, Bernardet JF, Segers P, Kersters K, Holmes B. 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. Zhang Z, Yang LL, Li CJ, Jiang XW, Zhi XY. Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis. Arch Microbiol 2021; 203:4777–4783 [View Article] [PubMed]
     [Google Scholar]
  3. Ilardi P, Fernández J, Avendaño-Herrera R. Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish. Int J Syst Evol Microbiol 2009; 59:3001–3005 [View Article] [PubMed]
     [Google Scholar]
  4. 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]
  5. Montero-Calasanz MDC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article] [PubMed]
     [Google Scholar]
  6. Du J, Ngo HTT, Won K, Kim K-Y, Jin F-X et al. Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:2372–2377 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. Nde AL, Charimba G, Hitzeroth A, Oosthuizen L, Steyn L et al. Chryseobacterium pennae sp. nov., isolated from poultry feather waste. Int J Syst Evol Microbiol 2021; 71:004912 [View Article] [PubMed]
     [Google Scholar]
  9. Son Y, Min J, Park W. Chryseobacterium faecale sp. nov., isolated from camel feces. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  10. Kong D, Wang Y, Li Q, Zhou Y, Jiang X et al. Chryseobacterium subflavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  11. Sang MK, Jeong JJ, Kim J, Kim KD. Growth promotion and root colonisation in pepper plants by phosphate-solubilising Chryseobacterium sp. strain ISE14 that suppresses Phytophthora blight. Ann Appl Biol 2018; 172:208–223 [View Article]
     [Google Scholar]
  12. Chhetri G, Kim I, Kim J, So Y, Seo T. Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula). J Antibiot 2022; 75:312–320 [View Article]
     [Google Scholar]
  13. Kang M, Chhetri G, Kim J, Kim I, So Y et al. Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  14. So Y, Chhetri G, Kim I, Kang M, Kim J et al. Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  15. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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] [PubMed]
     [Google Scholar]
  16. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  17. Kim I, Chhetri G, Kim J, So Y, Seo T. Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Kim I, Chhetri G, Kim J, Kang M, So Y et al. Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang waterfall on Jeju Island. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  26. Chhetri G, Seo T. Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang waterfall, Jeju Island. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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] [PubMed]
     [Google Scholar]
  29. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008; 9: [View Article]
     [Google Scholar]
  30. 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] [PubMed]
     [Google Scholar]
  31. 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]
  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] [PubMed]
     [Google Scholar]
  33. 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]
  34. Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079–1085 [View Article] [PubMed]
     [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  36. Chhetri G, Kim J, Kim I, Kang M, Lee B. Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
     [Google Scholar]
  37. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article]
     [Google Scholar]
  38. Smibert RM, Kreig NR. Phenotypic characterization. In Gerhardt P, Murray R, W W, Kreig N. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  39. Kim S-J, Ahn J-H, Weon H-Y, Hong S-B, Seok S-J et al. Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol 2015; 65:113–116 [View Article] [PubMed]
     [Google Scholar]
  40. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article] [PubMed]
     [Google Scholar]
  41. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  42. Kang M, Chhetri G, Kim J, Kim I, Seo T. Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  43. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  44. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  45. Loch TP, Faisal M. Chryseobacterium aahli sp. nov., isolated from lake trout (Salvelinus namaycush) and brown trout (Salmo trutta), and emended descriptions of Chryseobacterium ginsenosidimutans and Chryseobacterium gregarium. Int J Syst Evol Microbiol 2014; 64:1573–1579 [View Article] [PubMed]
     [Google Scholar]
  46. Kim KK, Lee KC, Oh HM, Lee JS. Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. Int J Syst Evol Microbiol 2008; 58:533–537 [View Article] [PubMed]
     [Google Scholar]
  47. Loveland-Curtze J, Miteva V, Brenchley J. Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles 2010; 14:61–69 [View Article] [PubMed]
     [Google Scholar]
  48. Pal M, Kumari M, Kiran S, Salwan R, Mayilraj S et al. Chryseobacterium glaciei sp. nov., isolated from the surface of a glacier in the Indian trans-Himalayas. Int J Syst Evol Microbiol 2018; 68:865–870 [View Article] [PubMed]
     [Google Scholar]
  49. Lucena T, Ruvira MA, Macián MC, Arahal DR, Aznar R. Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005989
Loading
Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil
Int J Syst Evol Microbiol 73, 005989 (2023); https://doi.org/10.1099/ijsem.0.005989
/content/journal/ijsem/10.1099/ijsem.0.005989
/content/journal/ijsem/10.1099/ijsem.0.005989
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