Polyphasic Characterization of Ca. Methylomicrobium oryzae: A Methanotroph Isolated from Rice Fields

Abstract

Global warming is the current threat to mankind and methane is the second most important greenhouse gas. Methanotrophs represent a group of bacteria that oxidize methane and are, therefore, environmentally very important. The cultivation of methanotrophs poses a challenge due to their specific cultivation conditions. Rice fields are important habitats where methanotrophs play a vital role in methane mitigation. We recently cultured Methylomicrobium strain RS1 from a rice field in India and briefly suggested it to be a member of putative novel species (Ca. Methylomicrobium oryzae) using draft genome-based ANI and DDH parameters (Rahalkar et al. in Front Microbiol 12:1-15, 2021). This culture presented challenges in terms of weak growth and inability to get cryopreserved. In the present work, we carried out the polyphasic characterization of this novel species which encompasses its chemotaxonomic, metabolic properties and salient genome features. Ca. Methylomicrobium oryzae is the first cultured methanotroph to be described from rice field habitats and could be an essential player in these ecosystems. It awaits further studies. Methylomicrobium sequences have been reported from rice fields but there were no reports of cultivation of members from this group, and this is the first report. Due to its growth challenges and fastidious nature of growth, inability to be cryo-preserved, and additionally due to legislations imposed on countries including India, the culture cannot be deposited in two international culture collections in other foreign countries. Within India, Ca. Methylomicrobium oryzae RS1 is maintained in our laboratory as a live culture at 4 °C and at room temperature (25-30 °C) by subculturing after intervals. Our laboratory is part of the WDCM approved culture collection MCM, and the culture is registered as MCMB-1473. It is also deposited in another internationally recognized culture collection: NCMR, Pune with the accession number MCC-4197. The draft genome of Ca. Methylomicrobium oryzae RS1 is available as JAERVK01.1.

Supplementary information: The online version contains supplementary material available at 10.1007/s12088-024-01381-9.

Keywords: Ca. Methylomicrobium oryzae; Methylomicrobium; Novel; Rice fields; Species.