1887

Abstract

Soybean pods, separated and enclosed from the outside environment, are considered a suitable place to find new microbes. A Gram-stain-negative, aerobic bacterium, bacterial strain (YB22) was isolated from the pod of (soybean) collected from a rural area in Republic of Korea and characterized by using polyphasic taxonomy. Cells of the strain were rod-shaped (approximately 0.4–0.6 µm wide and 4.0–5.0 µm long), non-flagellated and formed silver-yellow colonies. Cells grew at 25–35 °C (optimum, 28–30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and with 0–2.0% NaCl (optimum, 0 % NaCl). 16S rRNA gene sequencing showed that strain YB22 was phylogenetically closest to the genus , and showed highest similarities to G4070 (96.7 %), ATCC 13253 (96.7 %), DSM 14571 (96.6 %), G0146 (96.5 %), G4122 (96.4 %) and R26 (96.2 %). Average amino acid identity values between strain YB22 and other taxa in the genus were all above the threshold range of genus determination. Average nucleotide identity and digital DNA–DNA hybridization values between strain YB22 and other phylogenetic relatives were all found to be below the threshold range for species determination. The respiratory quinone of strain YB22 was menaquinone 6 (MK-6) and the predominant cellular fatty acids were iso-C (47.8 %) and iso-C 3-OH (18.5 %). The major polar lipids were phosphatidylethanolamine, four unidentified aminolipids and three unidentified polar lipids. The phylogenetic analysis and physiological and biochemical data showed that strain YB22 should represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain for this novel species is YB22 (=KCCM 43263=JCM 32097).

Funding
This study was supported by the:
  • Ministry of Education (Award 2020R1A6A1A03043283)
    • Principle Award Recipient: SangJoonMo
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2021-04-09
2022-09-25
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References

  1. Vandamme P, Bernardet J-F, 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. Kim KK, Kim MK, Lim JH, Park HY, Lee S-T. Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. Int J Syst Evol Microbiol 2005; 55:1287–1293 [View Article][PubMed]
    [Google Scholar]
  3. Kämpfer P, Busse H-J, McInroy JA, Glaeser SP. Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelis Kämpfer et al. 2011. Int J Syst Evol Microbiol 2015; 65:2187–2193 [View Article][PubMed]
    [Google Scholar]
  4. Doijad S, Ghosh H, Glaeser S, Kämpfer P, Chakraborty T. Taxonomic reassessment of the genus Elizabethkingia using whole-genome sequencing: Elizabethkingia endophytica Kämpfer et al. 2015 is a later subjective synonym of Elizabethkingia anophelis Kämpfer et al. 2011. Int J Syst Evol Microbiol 2016; 66:4555–4559 [View Article]
    [Google Scholar]
  5. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J et al. Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov. Antonie van Leeuwenhoek 2018; 111:55–72 [View Article][PubMed]
    [Google Scholar]
  6. Okazaki T. Studies on actinomycetes isolated from plant leaves. In Kurboke I. editor Selective Isolation of Rare Actinomycetes Canberra: National Library of Australia; 2003 pp 102–122
    [Google Scholar]
  7. 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][PubMed]
    [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley; 1991 pp 115–176
    [Google Scholar]
  9. 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]
  10. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [View Article][PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  15. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137–141 [View Article][PubMed]
    [Google Scholar]
  16. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–D462 [View Article][PubMed]
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003; 4:41 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article][PubMed]
    [Google Scholar]
  21. Lee I, Ouk Kim Y, Park S-C, 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]
  22. 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]
  23. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [View Article][PubMed]
    [Google Scholar]
  24. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  25. Marteyn BS, Karimova G, Fenton AK, Gazi AD, West N et al. ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics. mBio 2014; 5:e00022–14 [View Article][PubMed]
    [Google Scholar]
  26. Shi H, Bratton BP, Gitai Z, Huang KC. How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction. Cell 2018; 172:1294–1305 [View Article][PubMed]
    [Google Scholar]
  27. 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 607–653
    [Google Scholar]
  28. Barrow GI, Cowan FRKA. Steel’s Manual for Identification of Medical Bacteria Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  29. Bernardet JF, Nakagawa Y, Holmes B. 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]
  30. 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]
  31. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article][PubMed]
    [Google Scholar]
  32. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  34. 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]
  35. Collins MD, Goodfellow M, Minnikin DE, Alderson G. Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 1985; 58:77–86 [View Article][PubMed]
    [Google Scholar]
  36. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  37. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13:128–130 [View Article]
    [Google Scholar]
  38. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990b; 66:199–202 [View Article]
    [Google Scholar]
  39. Komagata K, Suzuki KI. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
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