Methylopila carotae sp. nov., a facultative methylotroph, isolated from a root of Daucus carota L.
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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).
KeywordsMethylopila 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.
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.
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.
- 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
- 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
- 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
- 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
- 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
- Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193(1):265–275Google Scholar
- 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
- 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
- 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
- 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