Edaphocola flava sp. nov., Isolated from Herbicide Bensulfuron-methyl-Contaminated Soil

  • Ting Hu
  • Yun Xiang
  • Zi-Yu Xing
  • Peng Qi
  • Xing HuangEmail author


A novel strain, HME-24T, was isolated from herbicide bensulfuron-methyl-contaminated soil in Jiangning District, Jiangsu Province, China. Strain HME-24T was a Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, and the colonies on R2A agar are yellow. The strain was non-sporulating, catalase- and oxidase-positive. Cells growth occurred at 15–37 °C (optimum, 30 °C), at pH 6.0–8.0 (optimum, 7.0) and with 0–1.5% (w/v) NaCl (optimum, 0.5% NaCl). Strain HME-24T showed the highest 16S rRNA gene sequence identity to Edaphocola aurantiacus H2T (99.58%), followed by Taibaiella chishuiensis AY17T (94.02%). The sole respiratory quinone was Menaquinone-7 (MK-7), the major polar lipids of strain HME-24T were two unidentified lipids, two unidentified aminolipids, an unidentified glycolipid and phosphatidylethanolamine, and the major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The genomic DNA G+C content values based on total genome sequences of strain HME-24T and H2T were 43.6 mol% and 43.8 mol%, respectively. Average nucleotide identity (ANI) for draft genomes between strain HME-24T and H2T was 94.8%, and the digital DNA–DNA hybridization (dDDH) for draft genomes between strain HME-24T and H2T was 59.2%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain HME-24T represents a novel species of the genus Edaphocola, with the name Edaphocola flava sp. nov. being proposed. The type strain of Edaphocola flava is HME-24T (= KCTC 62977T = CGMCC 1.13935T).



This work was funded by the National Natural Science Fund of China (41671317) and the Jiangsu Agriculture Science and Technology Innovation Fund (CX(18)1005).

Compliance with Ethical Standards

Conflict of interest

The authors declare that there are no conflicts of interest.

Research Involving Human Participants and/or Animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Electronic supplementary material 2 (SEQ 3669 kb)


  1. 1.
    Choi J, Cha S, Chhetri G, Yang D, Seo T (2019) Edaphocola aurantiacus gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from wetland soil in South Korea. Antonie Van Leeuwenhoek 112:687–694CrossRefGoogle Scholar
  2. 2.
    Fautz E, Reichenbach H (1980) A simple test for flexirubin type pigments. FEMS Microbiol Lett 8:87–91CrossRefGoogle Scholar
  3. 3.
    Barrow GI, Feltham RKA (1993) Cowan and steel’s manual for the identification of medical bacteria, 3rd edn. Cambridge University Press, Cambridge, pp 331–335CrossRefGoogle Scholar
  4. 4.
    Zhou XY, Zhang L, Su XJ, Hang P, Hu B, Jiang JD (2019) Sphingomonas flavalba sp nov, isolated from a procymidone-contaminated soil. Int J Syst Evol Microbiol 69:2937Google Scholar
  5. 5.
    Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–284Google Scholar
  6. 6.
    Nishijima M, Araki-sakai M, Sano H (1997) Identification of isoprenoid quinones by frit-fab liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28:113–122CrossRefGoogle Scholar
  7. 7.
    Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202CrossRefGoogle Scholar
  8. 8.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101Google Scholar
  9. 9.
    Yoon JH, Kim H, Kim SB, Kim HJ, Kim WY, Lee ST, Goodfellow M, Park YH (1996) Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Evol Microbiol 46:502–505Google Scholar
  10. 10.
    Lane DL (1991) 16S/23S rRNA sequencing. In nucleic acid techniques in bacterial systematics 115–175Google Scholar
  11. 11.
    Yoon SH, Ha SM, Kwon S (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar
  12. 12.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar
  13. 13.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  14. 14.
    Tamura K, Peterson D, Peterson N (2011) Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  15. 15.
    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
  16. 16.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  17. 17.
    Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714CrossRefGoogle Scholar
  18. 18.
    Li R, Zhu H, Ruan J, Qian W, Fang XD, Shi ZB, Li YR, Li ST, Shan G, Kristiansen K, Li SG, Yang HM, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272CrossRefGoogle Scholar
  19. 19.
    Meier-kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. Bioinformatics 14:60PubMedGoogle Scholar
  20. 20.
    Auch AF, Jan MV, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117CrossRefGoogle Scholar
  21. 21.
    Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572CrossRefGoogle Scholar
  22. 22.
    Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefGoogle Scholar
  23. 23.
    Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91CrossRefGoogle Scholar
  24. 24.
    Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar

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

Authors and Affiliations

  1. 1.College of Life SciencesNanjing Agricultural UniversityNanjingPeople’s Republic of China

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