Description of ‘Ca. Methylobacter oryzae’ KRF1, a novel species from the environmentally important Methylobacter clade 2

• Published in: Antonie van Leeuwenhoek 2020-05, Vol.113 (5), p.729-735
• Main Authors: Khatri, Kumal, Mohite, Jyoti A., Pandit, Pranitha S., Bahulikar, Rahul, Rahalkar, Monali C.
• Format: Article
• Language: English
• Subjects: Biomedical and Life Sciences; Cell culture; Cell walls; Collection; Cryopreservation; Culture collections; Deoxyribonucleic acid; DNA; Esters; Fatty acid methyl esters; Fatty acids; Gene sequencing; Genomes; Hybridization; Life Sciences; Medical Microbiology; Methanotrophic bacteria; Methylobacter; Microbiology; Microorganisms; Nucleotides; Phylogeny; Plant Sciences; Short Communication; Soil Science & Conservation
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-019-01369-2

Members of the genus Methylobacter ( Mtb ) have been identified to be the most dominant methanotrophs in aquatic as well as terrestrial habitats. Methylobacter shows four species with validly published names and these are grouped in two clades based on phylogenetic and genomic comparisons. Mtb luteus and Mtb marinus (synonym: Mtb whittenburyi ) belong to clade 1 Methylobacter . Clade 2 Methylobacter comprises of two species: Mtb tundripaludum and Mtb psychrophilus (type strain, no longer available). We isolated a yellow pigmented, rod-shaped methanotroph, strain (KRF1), from a tropical rice field in India, which might represent a putative novel species within Methylobacter clade 2. The cells are long, thick and motile rods. The strain grows under variable oxygen concentration (5–80% air) and also in nitrogen free media (5–50% air). The morphological, chemotaxonomic and genomic features of KRF1 were investigated in details. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) comparisons with the members of its closest species, Mtb tundripaludum , were in the range of 20–26% and ~ 73–81%, respectively. The fatty acid methyl esters profile of KRF1 was different from the profile of Mtb tundripaludum SV96 T . The major cell wall fatty acids of strain KRF1 are 16:1 ω7c/16:1 ω6c summed feature (55.4%) and 16:1 ω5c (28.6%). The draft genome of KRF1 is of 5.04 Mbp in size with a GC content of 49.3% and the whole genome shotgun sequencing project has the accession number RYFG00000000 (version: RYFG02000000). Due to the difficulties in the maintenance and cryopreservation of this culture, it could not be deposited in two international culture collections. We thereby propose KRF1 to be member of a Candidatus species, ‘ Candidatus Methylobacter oryzae’ KRF1. The culture is maintained live in our laboratory and also in our institutional WDCM approved culture collection (MACS Collection of Microorganisms) as MCMB-1471.