Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column

Abstract

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs), in the Planctomycetota, Verrucomicrobiota, and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse, and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.

Novel, active, and uncultured hydrocarbon degrading microbes in the ocean

“…This suggests that methane oxidation is mediated by previously unrecognized microbes, that in the case of Colwellia and until recently, Cycloclasticus , are outside of the canonical methanotrophic clades that are typically thought to carry out this reaction. This is similar to the recent findings of active, non-canonical methanotrophs that were reported in the GOM (Howe et al 2023). Further, the fact that all Cycloclasticus encoded methane oxidation, regardless of where it was sampled from, further supports its taxonomic placement as a family in the Methylococcales , a microbial group that has become a paradigm of marine methane oxidation.…”

Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils

“…In extreme environments (high temperature or low pH), methanotrophy is carried out by microorganisms of the phylum Verrucomicrobiota [12], known as Type III [8]. Non-canonical MOBs are also distributed in other phyla, such as Actinobacteria [13], Planctomycetota, and one putative Latescibacterota [14]. The first step of aerobic CH 4 oxidation is catalyzed by methane monooxygenases, either in particulate or soluble forms [15].…”