Description and salient genome characteristics of a putative novel species Methylomonas strain WWC4, isolated from an Indian freshwater ecosystem

Abstract

Freshwater wetlands are interesting habitats for methane-oxidizing bacteria or methanotrophs. We isolated a methanotroph, strain WWC4, from the mud of a freshwater creek running close to a beach in the coastal regions of Western India, near Alibag town. Strain WWC4 was a strict methanotroph, thriving only on methane and marginally on methanol. It formed pink to slightly orange-colored round colonies and formed pinkish turbidity or surface pellicle in liquid culture, indicative of the Methylomonas genus. The strain is characterized by thick, short, and motile rods, 2.5-3 µm long and 0.8-1.2 µm wide in size, with a Gram-negative character. Based on the 16S rRNA gene sequence, the culture was classified as a Methylomonas strain, with the nearest type species being Methylomonas koyamae Fw12E-YT showing 97.81% sequence similarity. A comparison of the draft genomes indicated that Methylomonas sp. WWC4 genome showed only 74.45%, 75.72%, and 21.5% similarities of AAI, ANIb, and dDDH values, respectively, with its closest neighbor Methylomonas koyamae Fw12E-YT, indicating its taxonomic novelty at the level of species. The GC content of the genome was 55.9 mol%. The whole-genome shotgun project was deposited at DDBJ/ENA/GenBank, and the accession number is JAATWI01.1. The cell wall lipids indicated a unique fingerprint with 15:1 ω8c (21.09%), 16:0 3OH (15.7%), and 16:1ω5c (12.6%) being the primary fatty acids, dissimilar to any other related Methylomonas species, confirming its taxonomic novelty. The genome was further explored for carotenoid pathways and plant growth promotion genes for its biotechnological potential. Strain WWC4 did not withstand cryopreservation and could not be deposited in two international culture collections. The culture is part of our institutional, WDCM-approved culture collection as MCMB-1474, maintained live. Due to its taxonomical novelty, strain WWC4 is also proposed to be a member of a Candidatus species of the Methylomonas genus and named “Candidatus Methylomonas sedimenticola” strain WWC4.