Methylopila carotae sp. nov., a facultative methylotroph, isolated from a root of Daucus carota L.

  • Elena N. Kaparullina
  • Alina A. Chemodurova
  • Nadezhda V. Agafonova
  • Tatiana A. Karataeva
  • Ekaterina N. Detkova
  • Yuri A. Trotsenko
  • Nina V. DoroninaEmail author
Original Paper


An aerobic facultatively methylotrophic bacterium, designated strain Das4.1T, was isolated from a root of Daucus carota L. The cells of this strain were observed to be Gram-stain negative, asporogenous, non-motile short rods multiplying by binary fission. Strain Das4.1T can utilise methanol, methylamine and a variety of polycarbon compounds as carbon and energy sources. C1-compounds were found to be assimilated via the isocitrate lyase-negative variant of the serine pathway. On medium with 0.5% methanol, growth of strain Das4.1T was observed at pH 5.5–9.0 (optimum, pH 6.0–7.0) and 18–37 °C (optimum, 24–29 °C) and in the presence of 0–2% (w/v) NaCl (optimum, 0.05%). Cells are catalase and oxidase positive and synthesise indole from l-tryptophan. The major fatty acids of methanol-grown cells were identified as C18:1ω7c, C18:0 and 11-methyl-C18:1ω7c. The predominant phospholipids were found to be phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The major respiratory quinone was identified as Q-10. The DNA G + C content of strain Das4.1T was determined to be 67.3 mol% (Tm). Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain Das4.1T belongs to the genus Methylopila and shows high sequence similarity to Methylopila oligotropha 2395AT (98.4%) and Methylopila capsulata IM1T (98.0%). However, the DNA–DNA relatedness of strain Das4.1T with M. oligotropha 2395AT was only 22 ± 3%. Based on genotypic, chemotaxonomic and physiological characterisation, the isolate can be classified as a novel species of the genus Methylopila, for which the name Methylopila carotae sp. nov. is proposed. The type strain is Das4.1T (= VKM B-3244T = CCUG 72399T).


Methylopila carotae sp.nov. Taxonomy Phytosymbiont 



We are grateful to Drs N.E. Suzina (Laboratory of cytology of microorganisms, IBPM RAS) for determination of the cell morphology by electron microscopy and N.V. Prisyazhnaya (All-Russian Collection of Microorganisms, IBPM RAS) for MALDI analysis.

Authors’ contributions

EK analysed most of the data and wrote the initial draft of the paper. YT and ND contributed to providing critical revisions to this article. AC, NA TK were responsible for collecting samples and to carrying out physiological analyses. ED was responsible for DNA–DNA hybridization and GC analyses. All authors discussed the results and revised the manuscript.


The work was supported by the grant of the Russian Foundation for Basic Research RFBR 16-04-00381_a.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

This article does not contain any studies with human participants and/or animals performed by any of the authors. The formal consent is not required in this study.

Supplementary material

10482_2019_1263_MOESM1_ESM.pdf (273 kb)
Supplementary material 1 (PDF 273 kb)


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Elena N. Kaparullina
    • 1
  • Alina A. Chemodurova
    • 1
  • Nadezhda V. Agafonova
    • 1
  • Tatiana A. Karataeva
    • 2
  • Ekaterina N. Detkova
    • 3
  • Yuri A. Trotsenko
    • 1
  • Nina V. Doronina
    • 1
    Email author
  1. 1.IBPM RAS, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of SciencesFederal Research Center Pushchino Center for Biological Research of the Russian Academy of SciencesPushchino, Moscow RegionRussia
  2. 2.Institute of Cell Biophysics of the Russian Academy of SciencesFederal Research Center Pushchino Center for Biological Research, Russian Academy of SciencesPushchino, Moscow RegionRussia
  3. 3.Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of SciencesMoscowRussia

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