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Volume 73, Issue 9

gen. nov., sp. nov. and sp. nov., isolated from tree barks Open Access

Abstract

Two Gram-staining-negative, aerobic, rod-shaped, bacteria that formed pale-pinkish colonies, designated HMF7056 and HMF7647 were isolated from Ginkgo () and Korean cornel dogwood (), respectively. Phylogenetic analyses based on sequences of 16S rRNA genes and 92 core genes indicated that two strains represent novel species within the family . HMF7056 and HMF7647 showed high 16S rRNA sequence similarities to N7d-4 (93.9 % and 95.7 %, respectively). The genomes of HMF7056 and HMF7647 were 5.2 and 4.8 Mbp in size with 50.5 and 42.5 % DNA G+C contents, respectively. Menaquinone-7 was the main respiratory quinone. The predominant fatty acids of HMF7056 and HMF7647 were iso-C and summed feature 3 (Cω7 and/or Cω6). The major polar lipid of both strains was phosphatidylethanolamine. The average nucleotide identity and digital DNA–DNA hybridization values of HMF7056, HMF7647 and related species were well below the threshold limit for species delineation (<68.9 and <20.8 %, respectively). The average amino acid identity values of HMF7056, HMF7647 with related type strains were below 67.8 and 68.3 %, respectively. On the basis of the results of phenotypic and phylogenetic characterizations, the two strains are considered to represent members of a novel genus of the family , for which the names gen. nov., sp. nov. and sp. nov. are proposed. The type strains are HMF7056 (=KCTC 72282 =NBRC 113964) and HMF7647 (=KCTC 72283 =NBRC 113965), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16s rRNA gene , ginkgo , Hufsiella , Korean cornel dogwood and tree barks
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-09-27
2024-05-08
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References

  1. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In Krieg NR, Staley JT, DR B, Hedlund BP. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 4 New York: Springer; 2010 p 25
     [Google Scholar]
  2. Kämpfer P et al. Order I. Sphingobacteriales ord. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 4 New York: Springer; 2010 p 330
     [Google Scholar]
  3. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48 Pt 1:165–177 [View Article] [PubMed]
     [Google Scholar]
  4. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
     [Google Scholar]
  5. Lambiase A. The family Sphingobacteriaceae. In Rosenberg E, DeLong EF, Stachkbrandt E, Lory S, Thompson F. eds The Prokaryotes – Other Major Lineages of Bacteria and the Archaea Berlin: Springer-Verlag Heidelberg; 2014 pp 907–914
     [Google Scholar]
  6. Figueiredo G, Gomes M, Covas C, Mendo S, Caetano T. The unexplored wealth of microbial secondary metabolites: the Sphingobacteriaceae case study. Microb Ecol 2022; 83:470–481 [View Article] [PubMed]
     [Google Scholar]
  7. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014; 64:2431–2436 [View Article] [PubMed]
     [Google Scholar]
  8. Lee HG, Kim SG, Im WT, Oh HM, Lee ST. Pedobacter composti sp. nov., isolated from compost. Int J Syst Evol Microbiol 2009; 59:345–349 [View Article] [PubMed]
     [Google Scholar]
  9. Sun LN, Zhang J, Chen Q, He J, Li SP. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260–2264 [View Article] [PubMed]
     [Google Scholar]
  10. Kang H, Kim H, Bae S, Joh K. Mucilaginibacter arboris sp. nov., and Mucilaginibacter ginkgonis sp. nov., novel bacteria isolated from freshwater and tree bark. Int J Syst Evol Microbiol 2021; 71:004755
     [Google Scholar]
  11. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 125–175
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  19. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2012; 40:D115–22 [View Article] [PubMed]
     [Google Scholar]
  22. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  25. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Brown AE. Benson’s Microbiological Application Laboratory Manual in General Microbiology, 10th ed. New York: McGraw-Hill; 2007
     [Google Scholar]
  28. Alexander SK, Strete D. Microbiology: A Photographic Atlas for the Laboratory Benjamin Cummings; 2001
     [Google Scholar]
  29. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [View Article] [PubMed]
     [Google Scholar]
  30. 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 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Collins MD. Analysis of isoprenoid quinones. In Gottschalk G. eds Methods in Microbiology, 18 New York: Acad. Press; 1985 pp 329–366
     [Google Scholar]
  33. Jeon Y, Kim JM, Park JH, Lee SH, Seong C-N et al. Pedobacter oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2009; 59:2491–2495 [View Article] [PubMed]
     [Google Scholar]
  34. Oh H-W, Kim B-C, Park D-S, Jeong W-J, Kim H et al. Pedobacter luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:1304–1310 [View Article] [PubMed]
     [Google Scholar]
  35. Margesin R, Zhang DC. Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2013; 63:339–344 [View Article] [PubMed]
     [Google Scholar]
  36. Prasad S, Manasa BP, Buddhi S, Pratibha MS, Begum Z et al. Arcticibacter svalbardensis gen. nov., sp. nov., of the family Sphingobacteriaceae in the phylum Bacteroidetes, isolated from Arctic soil. Int J Syst Evol Microbiol 2013; 63:1627–1632 [View Article] [PubMed]
     [Google Scholar]
  37. Urios L, Intertaglia L, Magot M. Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer. Int J Syst Evol Microbiol 2013; 63:303–308 [View Article] [PubMed]
     [Google Scholar]
  38. Liu Q, Kim SG, Liu HC, Xin YH, Zhou YG. Arcticibacter pallidicorallinus sp. nov. isolated from glacier ice. Int J Syst Evol Microbiol 2014; 64:2229–2232 [View Article] [PubMed]
     [Google Scholar]
  39. Shen L, Liu Y, Gu Z, Yao T, Xu B et al. Arcticibacter eurypsychrophilus sp. nov., isolated from ice core. Int J Syst Evol Microbiol 2015; 65:639–643 [View Article]
     [Google Scholar]
  40. Wei Y, Wang B, Zhang L, Zhang J, Chen S. Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2018; 68:2523–2529 [View Article] [PubMed]
     [Google Scholar]
  41. Du J, Singh H, Ngo HTT, Won K-H, Kim K-Y et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article] [PubMed]
     [Google Scholar]
  42. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article] [PubMed]
     [Google Scholar]
  43. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article] [PubMed]
     [Google Scholar]
  44. Pankratov TA, Tindall BJ, Liesack W, Dedysh SN. Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. Int J Syst Evol Microbiol 2007; 57:2349–2354 [View Article] [PubMed]
     [Google Scholar]
  45. Urai M, Aizawa T, Nakagawa Y, Nakajima M, Sunairi M. Mucilaginibacter kameinonensis sp., nov., isolated from garden soil. Int J Syst Evol Microbiol 2008; 58:2046–2050 [View Article] [PubMed]
     [Google Scholar]
  46. Baik KS, Park SC, Kim EM, Lim CH, Seong CN. Mucilaginibacter rigui sp. nov., isolated from wetland freshwater, and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2010; 60:134–139 [View Article] [PubMed]
     [Google Scholar]
  47. Chen XY, Zhao R, Tian Y, Kong BH, Li XD et al. Mucilaginibacter polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2014; 64:1395–1400 [View Article] [PubMed]
     [Google Scholar]
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Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov., isolated from tree barks
Int J Syst Evol Microbiol 73, 006050 (2023); https://doi.org/10.1099/ijsem.0.006050
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