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. 2018 Dec;111(12):2473-2484. doi: 10.1007/s10482-018-1136-3. Epub 2018 Jul 31.

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'.

Keywords: India; Methanotrophs; Novel genus; Pale pink; Rice fields; Strain Sn10-6; ‘Candidatus Methylocucumis oryzae’.

MeSH terms

  • Aerobiosis / physiology
  • Bacterial Typing Techniques
  • Base Composition
  • Color
  • Crops, Agricultural / microbiology
  • DNA, Bacterial / genetics*
  • Fatty Acids / biosynthesis
  • Genome, Bacterial*
  • Genotype
  • India
  • Methane / metabolism
  • Methylococcaceae / classification
  • Methylococcaceae / genetics*
  • Methylococcaceae / isolation & purification
  • Methylococcaceae / metabolism
  • Oryza / microbiology*
  • Phenotype
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics*
  • Rhizosphere
  • Ubiquinone / biosynthesis

Substances

  • DNA, Bacterial
  • Fatty Acids
  • RNA, Ribosomal, 16S
  • Ubiquinone
  • Methane