Genome-based insights into a putative novel Methylomonas species (strain Kb3), isolated from an Indian rice field

Methylomonas is one of the most important and frequently detected genera in aquatic habitats and rice fields. A strain of Methylomonas, Kb3, an aerobic methanotroph, was isolated from a rice field from the Western parts of India. Kb3 cells were composed of short, motile rods and formed pink colored colonies and pink pellicles in liquid. On the basis of 16S rRNA gene, the closest valid species was Methylomonas methanica strain S1 (97.9% sequence similarity). Kb3 also showed close affiliation to “Methylomonas denitrificans” FJG1, a recently described, but not yet valid species (99.1% sequence similarity) and to strain LW13, a freshwater lake Washington isolate (99.5% sequence similarity). To understand the correct taxonomical position and metabolic properties of Kb3, the whole genome was sequenced. Kb3 genome showed a complete methane oxidation pathway, the presence of pMMO and sMMO genes, genes for nitrogen fixation and potential to convert nitrite to nitric oxide and nitric oxide to nitrous oxide. Numerous genes for chemotaxis and motility were detected. Genome comparison of Kb3 with the genomes of Methylomonas methanica S1 and “Methylomonas denitrificans” FJG1 showed ortho-ANI values of 86-87%, much less than 95%, the current cut-off for species. Digital DNA-DNA hybridization also showed values of 41-42%, much lesser than the 70% cut-off, both indicating that Kb3 did not belong to any of these species. Methylomonas LW13 and Methylomonas Kb3 showed close genome level similarities, i.e. OrthoANI value of 97.9% and a DDH of 87.3% and close branching in the phylogenomic tree confirming that Kb3 and LW13 can together form a new species.