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Geomonas soli gen. nov., sp. nov., a New Member of the Family Comamonadaceae, Isolated from Soil

  • Shehzad Abid Khan
  • Sang Eun Jeong
  • Hye Yoon Park
  • Sang-Suk Lee
  • Che Ok JeonEmail author
Article

Abstract

A Gram-stain negative, facultative aerobic bacterial strain, designated strain S-16T, was isolated from soil in South Korea. Colonies were white-milkish and cells were non-motile rods with oxidase- and catalase-positive activities. The growth of strain S-16T was observed at 20–40 °C (optimum, 25–30 °C) and pH 5.5–7.0 (optimum, pH 6.5). Ubiquinone-8 was identified as the sole respiratory quinone and C12:0, C16:0, C18:0, C15:1ω5c and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) were identified as the major fatty acids (>5%). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified polar lipid. The G + C content of the genomic DNA calculated from the whole genome sequence was 66.8 mol%. Strain S-16T was most closely related to Piscinibacter aquaticus IMCC1728T, Rhizobacter gummiphilus NS21T and Rhizobacter dauci H6T with 16S rRNA gene sequence similarities of 97.93%, 97.93% and 97.44%, respectively. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences suggested that strain S-16T could form a distinct phyletic lineage as a new genus within the family Comamonadaceae. Based on the phenotypic, chemotaxonomic and molecular features, strain S-16T represents the type strain of a novel species of a novel genus within the family Comamonadaceae, for which the name Geomonas soli gen. nov., sp. nov. is proposed. The type strain is S-16T (= KACC 19792T = JCM 32971T).

Notes

Acknowledgements

This work was supported by Grants from the National Institute of Biological Resources (NIBR201902203) (Grant Nos: NIBR No. 2019-02-001 and NIBR No. 201929201) of Ministry of Environment (MOE), Republic of Korea.

Compliance with Ethical Standards

Conflict of interest

The authors declare no competing financial conflicts of interests.

Ethical Approval

The authors have declared that no ethical issues exist.

Supplementary material

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Supplementary material 1 (DOCX 1882 kb)

References

  1. 1.
    Willems A, De Ley J, Gillis M, Kersters K (1991) Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Bacteriol 41:445–450CrossRefGoogle Scholar
  2. 2.
    Chen DZ, Yu NN, Chu QY, Chen J, Ye JX, Cheng ZW, Zhang SH, Chen JM (2018) Piscinibacter caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 68:2627–2632CrossRefGoogle Scholar
  3. 3.
    Shi YL, Sun Y, Jiang ZM, Ruan ZY, Su J, Yu LY, Zhang YQ (2019) Simplicispira lacusdiani sp. nov., a novel betaproteobacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 69:129–133CrossRefGoogle Scholar
  4. 4.
    Imai S, Yoshida R, Endo Y, Fukunaga Y, Yamazoe A, Kasai D, Masai E, Fukuda M (2013) Rhizobacter gummiphilus sp. nov., a rubber-degrading bacterium isolated from the soil of a botanical garden in Japan. J Gen Appl Microbiol 59:199–205CrossRefGoogle Scholar
  5. 5.
    Wang H, Li J, Hu A, Qin D, Xu H, Yu CP (2014) Melaminivora alkalimesophila gen. nov., sp. nov., a melamine-degrading betaproteobacterium isolated from a melamine-producing factory. Int J Syst Evol Microbiol 64:1938–1944CrossRefGoogle Scholar
  6. 6.
    Vaz-Moreira I, Narciso-da-Rocha C, Lopes AR, Carvalho G, Lobo-da-Cunha A, Whitman WB, Snauwaert C, Vandamme P, Manaia CM, Nunes OC (2017) Oryzisolibacter propanilivorax gen. nov., sp. nov., a propanil-degrading bacterium. Int J Syst Evol Microbiol 67:3752–3758CrossRefGoogle Scholar
  7. 7.
    Khan IU, Habib N, Asem MD, Salam N, Xiao M, Zhou EM, Zhi XY, Li WJ (2019) Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 69:337–342CrossRefGoogle Scholar
  8. 8.
    Lechner U, Brodkorb D, Geyer R, Hause G, Hartig C, Auling G, Fayolle-Guichard F, Piveteau P, Muller RH, Rohwerder T (2007) Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium. Int J Syst Evol Microbiol 57:1295–1303CrossRefGoogle Scholar
  9. 9.
    Zhang W-Y, Fang M-X, Zhang W-W, Xiao C, Zhang X-Q, Yu Z-P, Zhu X-F, Wu M (2013) Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae. Int J Syst Evol Microbiol 63:2062–2068CrossRefGoogle Scholar
  10. 10.
    Tanasupawat S, Takehana T, Yoshida S, Hiraga K, Oda K (2016) Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly (ethylene terephthalate). Int J Syst Evol Microbiol 66:2813–2818CrossRefGoogle Scholar
  11. 11.
    Fang W, Li Y, Xue H, Tian G, Wang L, Guo MW, Piao CG (2015) Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana. Int J Syst Evol Microbiol 65:3333–3338CrossRefGoogle Scholar
  12. 12.
    Lee Y, Park HY, Jeon CO (2019) Amnimonas aquatica sp. nov., isolated from a freshwater river. Curr Microbiol 76:478–484CrossRefGoogle Scholar
  13. 13.
    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 67:1613–1617CrossRefGoogle Scholar
  14. 14.
    Gomori G (1955) Preparation of buffers for use in enzyme studies. Methods Enzymol 1:138–146CrossRefGoogle Scholar
  15. 15.
    Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  16. 16.
    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 73:5261–5267CrossRefGoogle Scholar
  17. 17.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  18. 18.
    Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  19. 19.
    Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18CrossRefGoogle Scholar
  20. 20.
    Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595CrossRefGoogle Scholar
  21. 21.
    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 66:1100–1103CrossRefGoogle Scholar
  22. 22.
    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  23. 23.
    Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285CrossRefGoogle Scholar
  24. 24.
    Minnikin DE, O’Donnell A, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  25. 25.
    Komagata K, Suzuki KI (1988) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207CrossRefGoogle Scholar
  26. 26.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  27. 27.
    Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117CrossRefGoogle Scholar
  28. 28.
    Stackebrandt E, Verbarg S, Frühling A, Busse H-J, Tindall BJ (2009) Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium. Int J Syst Evol Microbiol 59:2552–2560CrossRefGoogle Scholar
  29. 29.
    Cho SH, Lee HJ, Jeon CO (2016) Piscinibacter defluvii sp. nov., isolated from a sewage treatment plant, and emended description of the genus Piscinibacter Stackebrandt et al. 2009. Int J Syst Evol Microbiol 66:4839–4843CrossRefGoogle Scholar
  30. 30.
    Wei L, Si M, Long M, Zhu L, Li C, Shen X, Wang Y, Zhao L, Zhang L (2015) Rhizobacter bergeniae nov., isolated from the root of Bergenia scopulosa. Int J Syst Evol Microbiol 65:479–484CrossRefGoogle Scholar
  31. 31.
    Jin L, Ko SR, Ahn CY, Lee HG, Oh HM (2016) Rhizobacter profundi sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 66:1926–1931CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Shehzad Abid Khan
    • 1
  • Sang Eun Jeong
    • 1
  • Hye Yoon Park
    • 1
    • 2
  • Sang-Suk Lee
    • 3
  • Che Ok Jeon
    • 1
    Email author
  1. 1.Department of Life ScienceChung-Ang UniversityDongjak-GuRepublic of Korea
  2. 2.National Institute of Biological ResourcesIncheonRepublic of Korea
  3. 3.Department of Animal Science and TechnologySunchon National UniversityJeonnamRepublic of Korea

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