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Volume 70, Issue 12

sp. nov., and sp. nov., novel bacteria isolated from birch tree () Free

Abstract

Two Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strains, designated as HMF7605 and HMF7616, were isolated from birch tree, in Yong-in, Republic of Korea. Strains HMF7605 and HMF7616 exhibited the highest 16S rRNA gene sequence similarities of 95.9 and 97.5 % to 17mud1-7, 97.9 % between themselves. The values of average nucleotide identity and DNA–DNA hybridization between strains HMF7605 and HMF7616 were 77.6 and 22.0 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains revealed that they belonged to the genus within the family . The predominant fatty acids of both strains were iso-C, summed feature 3 (comprising C c and/or C 6c), C 5c and summed feature 4 (comprising iso-C I and/or anteiso-C B). The both strains contained menaquinone-7 as the only isoprenoid quinone. The major polar lipid profiles of the two strains were similar with phosphatidylethanolamine, one unidentified aminophosphoglycolipid, one unidentified glycolipid and three unidentified polar lipids. The DNA G+C contents of strains HMF7605 and HMF7616 were 42.0 and 42.8 mol%, respectively. Based on the results of the phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, sp. nov. and sp. nov. are proposed. The type strains are HMF7605 (=KCTC 62465=NBRC 113228) and HMF7616 (=KCTC 62466=NBRC 113229), respectively.

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Keyword(s): Adhaeribacter pallidiroseus , Adhaeribacter arboris , Betula platyphylla and birch tree
© 2020 The Authors
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2020-10-16
2024-04-20
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References

  1. Rickard AH, Stead AT, O’May GA, Lindsay S, Banner M et al. Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm. Int J Syst Evol Microbiol 2005; 55:821–829 [View Article][PubMed]
     [Google Scholar]
  2. Zhang JY, Liu XY, Liu SJ. Adhaeribacter terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2009; 59:1595–1598 [View Article][PubMed]
     [Google Scholar]
  3. Weon HY, Kwon SW, Son JA, Kim SJ, Kim YS et al. Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples. Int J Syst Evol Microbiol 2010; 60:2424–2429 [View Article][PubMed]
     [Google Scholar]
  4. Elderiny N, Lee JJ, Lee YH, Park SJ, Lee SY et al. Adhaeribacter terrae sp. nov., a novel bacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:2922–2927 [View Article][PubMed]
     [Google Scholar]
  5. Kim DU, Kim KW, Kang MS, Kim JY, Jang JH et al. Adhaeribacter swui sp. nov., isolated from wet mud. Int J Syst Evol Microbiol 2018; 68:1096–1100 [View Article][PubMed]
     [Google Scholar]
  6. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 125–175
     [Google Scholar]
  7. Yoon SH, Ha SM, 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]
  8. 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]
  9. 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]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. 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]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  14. Na SI, Kim YO, Yoon SH, Ha SM, 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]
  15. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005; 33:W686–W689 [View Article][PubMed]
     [Google Scholar]
  16. Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 2015; 43:D130–D137 [View Article][PubMed]
     [Google Scholar]
  17. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  18. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000; 28:45–48 [View Article][PubMed]
     [Google Scholar]
  19. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article][PubMed]
     [Google Scholar]
  20. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
     [Google Scholar]
  21. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014; 42:D199–D205 [View Article][PubMed]
     [Google Scholar]
  22. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article][PubMed]
     [Google Scholar]
  23. Yoon SH, Ha SM, 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]
  24. 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]
  25. Hucker GJ. A new modification and application of the Gram stain. J Bacteriol 1921; 6:395–397 [View Article][PubMed]
     [Google Scholar]
  26. Brown AE. Benson’s Microbiological Application Laboratory Manual in General Microbiology, 10th ed. New York: McGraw-Hill; 2007
     [Google Scholar]
  27. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 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]
  28. Schmidt K, Connor A, Britton G. Analysis of pigments: carotenoids and related polyenes. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: John Wiley and Sons; 1994 pp 403–461
     [Google Scholar]
  29. CLSI Performance standards for antimicrobial disk susceptibility testing: approved standard. CLSI document M02-A11, 11th ed. PA: Clinical and Laboratory Standards Institute; 2012
     [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [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. editor Methods in Microbiology vol. 18 New York: Acad. Press; 1985 pp 329–366
     [Google Scholar]
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Adhaeribacter arboris sp. nov., and Adhaeribacter pallidiroseus sp. nov., novel bacteria isolated from birch tree (Betula platyphylla)
Int J Syst Evol Microbiol 70, 6195 (2020); https://doi.org/10.1099/ijsem.0.004516
/content/journal/ijsem/10.1099/ijsem.0.004516
/content/journal/ijsem/10.1099/ijsem.0.004516
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