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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
  • 17 Downloads

Abstract

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).

Keywords

Methylopila carotae sp.nov. Taxonomy Phytosymbiont 

Notes

Acknowledgements

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.

Funding

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)

References

  1. Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YuA (2015) Methylopila turkiensis sp. nov., a new aerobic facultatively methylotrophic phytosymbiont. Microbiology 84(4):544–552.  https://doi.org/10.1134/S0026261715040025 (Russian) CrossRefGoogle Scholar
  2. Anthony C, Williams P (2003) The structure and mechanism of methanol dehydrogenase. Biochim Biophys Acta 1647(1–2):18–23.  https://doi.org/10.1016/S1570-9639(03)00042-6 CrossRefGoogle Scholar
  3. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461–466.  https://doi.org/10.1099/ijsem.0.002516 CrossRefGoogle Scholar
  4. Collins MD (1985) Analysis of isoprenoid quinones. In: Gottschalk G (ed) Methods in microbiology, vol 18. Academic Press, New York, pp 329–366.  https://doi.org/10.1016/S0580-9517(08)70480-X Google Scholar
  5. De Ley J, Cattoir H, Reynaerts AJ (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12(1):133–142.  https://doi.org/10.1111/j.1432-1033.1970.tb00830.x CrossRefGoogle Scholar
  6. Doronina NV, Trotsenko YA, Krausova VI, Boulygina ES, Tourova TP (1998) Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium. Int J Syst Bacteriol 48(4):1313–1321.  https://doi.org/10.1099/00207713-48-4-1313 CrossRefGoogle Scholar
  7. Doronina NV, Trotsenko YA, Tourova TP, Kuznetsov BB, Leisinger T (2001) Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane. Int J Syst Bacteriol 51(3):1051–1058.  https://doi.org/10.1099/00207713-51-3-1051 CrossRefGoogle Scholar
  8. Doronina NV, Kaparullina EN, Bykova TV, Trotsenko YA (2013) Methylopila musalis sp. nov., a new aerobic facultatively methylotrophic bacterium isolated from banana fruit. Int J Syst Evol Microbiol 63(5):1847–1852.  https://doi.org/10.1099/ijs.0.042028-0 CrossRefGoogle Scholar
  9. Doronina NV, Kaparullina EN, Trotsenko YuA (2014) Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring. Int J Syst Evol Microbiol 64(1):158–164.  https://doi.org/10.1099/ijs.0.055046-0 CrossRefGoogle Scholar
  10. Doronina N, Torgonskaya M, Fedorov D, Trotsenko YA (2015) Aerobic methylobacteria as promising objects of modern biotechnology. Appl Biochem Microbiol 51(2):125CrossRefGoogle Scholar
  11. Doronina NV, Kaparullina EN, Chemodurova AA, Trotsenko YuA (2018) Paracoccus simplex sp. nov., a new methylamine-utilizing facultative methylotroph. Microbiology 87:662–671.  https://doi.org/10.1134/S0026261718050077 (Russian) CrossRefGoogle Scholar
  12. Fedorov DN, Doronina NV, Trotsenko YA (2011) Phytosymbiosis of aerobic methylobacteria: new facts and views. Microbiol (Moscow) 80(4):443–454.  https://doi.org/10.1134/S0026261711040047 CrossRefGoogle Scholar
  13. Gordon SA, Weber RP (1951) Colorimetric estimation of indole-acetic acid. Plant Physiol 26(4):192–195CrossRefGoogle Scholar
  14. Horneffer V, Haverkamp J, Janssen HG, Steeg PF, Notz R (2004) MALDI-TOF-MS analysis of bacterial spores: wet heat-treatment as a new releasing technique for biomarkers and the influence of different experimental parameters and microbiological handling. J Am Soc Mass Spectrom 15(10):1444–1454.  https://doi.org/10.1016/j.jasms.2006.07.002 CrossRefGoogle Scholar
  15. Kates M (1972) Techniques of lipidology. American Elsevier Publishing, New YorkCrossRefGoogle Scholar
  16. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64(2):346–351.  https://doi.org/10.1099/ijs.0.059774-0 CrossRefGoogle Scholar
  17. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  18. Li L, Zheng JW, Hang BJ, Doronina NV, Trotsenko YA, He J, Li SP (2011) An aerobic, facultatively methylotrophic bacterium. Int J Syst Evol Microbiol 61(7):1561–1566.  https://doi.org/10.1099/ijs.0.020925-0 CrossRefGoogle Scholar
  19. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193(1):265–275Google Scholar
  20. McDonald IR, Murrell JC (1997) The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microbiol 63:3218–3224Google Scholar
  21. Owen RJ, Lapage SP (1976) The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic applications. J Appl Bacteriol 41(2):335–340CrossRefGoogle Scholar
  22. Poroshina MN, Doronina NV, Kaparullina EN, Kovalevskaya NP, Trotsenko YA (2013) Halophilic and halotolerant aerobic methylobacteria from the technogenic Solikamsk biotopes. Microbiology 82(4):490–498 ((Moscow)) CrossRefGoogle Scholar
  23. Shmareva MN, Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA (2016) Emended descriptions of Advenella kashmirensis subsp. kashmirensis subsp. nov., Advenella kashmirensis subsp. methylica subsp. nov., and Methylopila turkiensis sp. nov. Microbiology 85(5):646–648 (Moscow) CrossRefGoogle Scholar
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729CrossRefGoogle Scholar
  25. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680CrossRefGoogle Scholar
  26. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes Int. J Syst Evol Microbiol 60:249–266CrossRefGoogle Scholar
  27. Van de Peer Y, De Wachter R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10(5):569–570Google Scholar
  28. Wang YN, Tian WY, He WH, Chen GC, An ML, Jia B, Liu L, Zhou Y, Liu SJ (2015) Methylopila henanense sp. nov., a novel methylotrophic bacterium isolated from tribenuron methyl-contaminated wheat soil. Antonie van Leeuwenhoek 107(2):329–336CrossRefGoogle Scholar
  29. Yang LQ, Liu L, Salam N, Xiao M, Kim CJ, Hozzein WN, Park DJ, Li WJ, Zhang HW (2016) Chenggangzhangella methanolivorans gen. nov., sp. nov., a member of the family Methylocystaceae, transfer of Methylopila helvetica Doronina et al. 2000 to Albibacter helveticus comb. nov. and emended description of the genus Albibacter. Int J Syst Evol Microbiol 66(8):2825–2830.  https://doi.org/10.1099/ijsem.0.001062 Google Scholar
  30. 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(5):1613–1617CrossRefGoogle Scholar

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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