Genomic Insights into a Versatile Deep-Sea Methanotroph Constituting the Rare Biosphere of a Brazilian Carbonate Mound Complex

Abstract

Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions, and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments. Phylogenomic analysis revealed <95% ANI to described species, with genomic evidence of deep-sea specialization including: (1) stress adaptation through cold-shock proteins (CspA) and DNA repair systems (UvrD/LexA), (2) metabolic versatility via complete methane oxidation (pmoABC), nitrogen fixation (nifHDK), and sulfur cycling (sox/sqr) pathways, and (3) niche partitioning through biofilm formation (GGDEF/EAL) and heavy metal resistance (CopZ/CzcD). Comparative genomics identified a 1,234-gene deep-sea core shared with M. sp. wino1, enriched in mobile elements (TnpA, prophages) suggesting horizontal gene transfer drives adaptation. While undetected in situ amplicon surveys, M. crucis exhibited rapid enrichment under methane availability, demonstrating its role as a latent methane filter. These findings contribute for the understanding of the ecological significance of aerobic methanotrophs in deep-sea systems, revealing how rare microbial taxa with genomic plasticity have the potential to influence biogeochemical cycling in deep carbonate-rich environments.