Methylobacter arcticus sp. nov. isolated from a coal mine biofilm in the high Arctic Svalbard

Abstract

An aerobic methanotroph was isolated from a biofilm of coal mine Gruve 7 (Svalbard) and designated strain G7T. Cells of strain G7T were Gram-stain-negative, pink-pigmented and motile rods. Strain G7T could grow at pH 6.8 and at temperatures ranging from 4 to 21 °C. The genome size was 4.00 Mb with a (digital) DNA G+C content of 47.7 mol%. Strain G7T represents a member of the family Methylomonadaceae of the class Gammaproteobacteria. It displayed 94.6-99.7% 16S rRNA gene sequence similarity to the type strains of the genus Methylobacter. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) confirmed that strain G7T represents a novel species. It showed 16S rRNA gene identity of 99.7%, 91.8% ANI and 46% dDDH to the closest type strain, Methylobacter svalbardensis LS7-T4AT, with ANI and dDDH being much lower than the typically used 95 and 70% cutoffs, respectively, to delineate different species. For methane activation, strain G7T carries genes encoding particulate methane monooxygenase (pmoCAB). Also, genes of the methane utilization pathways, i.e. oxidation of methane to carbon dioxide and assimilation of methane-carbon to biomass, were encoded in the genome. Strikingly, compared to all other Methylobacter spp. strains, strain G7T did not have nitrogenase genes for nitrogen fixation. Strain G7T also possessed genes for ectoine production, which was not observed in the genomes of its closest relatives. Based on phenotypic, genetic and phylogenetic data, strain G7T represents a novel species within the genus Methylobacter for which the name Methylobacter arcticus sp. nov. is proposed, with strain G7T (DSM: 117899; LMG: 33632) as the type strain.