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Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field

Abstract

An elliptical to cucumber-shaped methanotroph with large cells was isolated from a rice rhizosphere in Western India. Strain Sn10-6 is one of the first methanotrophs to be isolated from Indian rice fields. Cells of Sn10-6 are Gram-negative, motile, large in size (3–6 µm × 1.5–2 µm) and contain intracellular cytoplasmic membrane stacks. Colonies of Sn10-6 and liquid cultures have a pale pink colour. Strain Sn10-6 was initially isolated under micro-oxic conditions but later adapted to grow under fully oxic conditions. The major fatty acids present were identified as C16:1ω6c, C16:1ω7c and C16:0 and ubiquinone was found to be the major quinone. The 16S rRNA gene sequence of strain Sn10-6 displays high similarity to the genes of Methylovulum psychrotolerans Sph1T (93.6%) followed by Methylosarcina fibrata AML-C10T (93.5%) and about 90–93% similarity to the genes of known species of Type I methanotrophic genera from the family Methylococcaceae. The draft genome information indicated that the G + C content of strain Sn10-6 is 43.9 mol%. Phylogenetic trees using 16S rRNA gene and the particulate methane mono-oxygenase sequences unequivocally placed Sn10-6 close to the genus Methylovulum. Based on the 16S rRNA gene differences, morphological characters and draft genome information, strain Sn10-6 (=MCC 3492 =KCTC 15683) is described here as the type strain of a novel species within a new genus, ‘Candidatus Methylocucumis oryzae’.

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Acknowledgements

The work was supported by funds from DBT BioCARe, India and institutional funds received from MACS Agharkar Research Institute, India. We acknowledge the farmer, Mr. Rengde who supported the rice field sample collection. We also acknowledge Ms. Aditi Purandare, Ms. Vishakha Kulkarni and Dr. Neelima Kulkarni for their help during collection of the sample. We acknowledge Dr. Prashant K. Dhakephalkar for his support during the project.

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Correspondence to Monali C. Rahalkar.

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Pandit, P.S., Hoppert, M. & Rahalkar, M.C. Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field. Antonie van Leeuwenhoek 111, 2473–2484 (2018). https://doi.org/10.1007/s10482-018-1136-3

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Keywords

  • Methanotrophs
  • India
  • Rice fields
  • Candidatus Methylocucumis oryzae’
  • Novel genus
  • Pale pink
  • Strain Sn10-6