Viral potential to modulate microbial methane metabolism varies by habitat

Abstract

Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0–7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.

Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics

“…Methanogens use H 2 , methyl compounds, or acetates as sources for growth and methanogenesis [ 46 , 47 ]. The key functional gene in methane production is methyl-coenzyme M reductase (mcrA), which is responsible for the final step of methane production in methanogenesis and the activation reaction in methane oxidation metabolism [ 48 , 49 ]. It exists no matter how methane is produced.…”