Flavihumibacter soli sp. nov., Isolated from Soil

Abstract

A novel Gram-stain-positive, strictly aerobic, non-motile, rod-shaped bacterium, designated strain R14T was isolated from steep grove soil and taxonomically characterized using a polyphasic approach. Cells showed oxidase-negative and catalase-positive activities and grew at 25–37 °C (optimum, 30 °C), pH 5.0–8.0 (optimum, pH 6.5), and in the presence of 0–0.5% (w/v) NaCl (optimum, 0%). Phylogenetic trees based on 16S rRNA gene sequences revealed that strain R14T formed a phylogenetic lineage with Flavihumibacter genus members within the family Chitinophagaceae. Comparison of 16S rRNA gene sequences showed that strain R14T shared highest similarities with Flavihumibacter solisilvae 3-3T (97.5%), Flavihumibacter petaseus NBRC 106054T (96.7%), and Flavihumibacter stibioxidans YS-17T (96.1%). The G+C content of strain R14T calculated from its whole genome sequence was 44.6 mol%. Strain R14T contained menaquinone-7 and iso-C15:0, iso-C17:0 3-OH, C16:0, C15:1 ω6c, and iso-C15:0-G as the sole respiratory isoprenoid quinone and major cellular fatty acids, respectively. Major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phenotypic, and chemotaxonomic characteristics of strain R14T, it could be concluded that strain R14T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter soli sp. nov. is proposed. The type strain is R14T (=KACC 21229T = JCM 33473T).

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References

  1. 1.

    Zhang NN, Qu JH, Yuan HL, Sun YM, Yang JS (2010) Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. Int J Syst Evol Microbiol 60:1609–1612

    CAS  Article  Google Scholar 

  2. 2.

    Lee HJ, Jeong SE, Cho MS, Kim SH, Lee SS, Lee BH, Jeon CO (2014) Flavihumibacter solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 64:2897–2901

    CAS  Article  Google Scholar 

  3. 3.

    Han Y, Zhang F, Wang Q, Zheng S, Guo W, Feng L, Wang G (2016) Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil. Int J Syst Evol Microbiol 66:4676–4680

    CAS  Article  Google Scholar 

  4. 4.

    Kim WH, Lee S, Ahn TY (2014) Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream. Int J Syst Evol Microbiol 64:3235–3239

    CAS  Article  Google Scholar 

  5. 5.

    Lee DH, Cha CJ (2016) Flavihumibacter sediminis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 66:4310–4314

    CAS  Article  Google Scholar 

  6. 6.

    Kim J, Kim KH, Chun BH, Khan SA, Jeon CO (2020) Flagellimonas algicola sp. nov., isolated from a marine red alga, Asparagopsis taxiformis. Curr Microbiol 77:294–299

    CAS  Article  Google Scholar 

  7. 7.

    Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    CAS  Article  Google Scholar 

  8. 8.

    Feng T, Jeong SE, Lim JJ, Hyun S, Jeon CO (2019) Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond. J Microbiol 57:232–237

    CAS  Article  Google Scholar 

  9. 9.

    Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    CAS  Article  Google Scholar 

  10. 10.

    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    CAS  Article  Google Scholar 

  11. 11.

    Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, Tang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18

    Article  Google Scholar 

  12. 12.

    Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    CAS  Article  Google Scholar 

  13. 13.

    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  14. 14.

    Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  15. 15.

    Fautz E, Reichenbach H (1980) A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8:87–91

    CAS  Article  Google Scholar 

  16. 16.

    Lányi B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67

    Google Scholar 

  17. 17.

    Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  18. 18.

    Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

    CAS  Article  Google Scholar 

  19. 19.

    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI, Inc., Newark

    Google Scholar 

  20. 20.

    Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    CAS  Article  Google Scholar 

  21. 21.

    Zhou G, Chen C, Jeon CO, Wang G, Li M (2015) High quality draft genomic sequence of Flavihumibacter solisilvae 3-3T. Stand Genomic Sci 10:66

    Article  Google Scholar 

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Acknowledgements

This work was supported by the National Research Foundation (2017M3C1B5019250) of the Ministry of Science and ICT and the National Institute of Biological Resources (NIBR202002203), funded by the Ministry of Environment (MOE), Republic of Korea.

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YLS isolated the type strain from soil and YLS and JJ performed the experiments. SAK and KHK analyzed the genome and constructed phylogenetic trees. COJ supervised all works. YLS and COJ wrote the manuscript. The manuscript has been reviewed and edited by all authors.

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Correspondence to Che Ok Jeon.

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The GenBank Accession Numbers for the 16S rRNA gene and genome sequences of strain R14T are MN086351 and JAAFZB000000000, respectively.

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Seo, Y.L., Jung, J., Khan, S.A. et al. Flavihumibacter soli sp. nov., Isolated from Soil. Curr Microbiol (2020). https://doi.org/10.1007/s00284-020-02103-2

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