Viral potential to modulate microbial methane metabolism varies by habitat

Zhong, Zhi-Ping; Du, Jingjie; Köstlbacher, Stephan; Pjevac, Petra; Orlić, Sandi; Sullivan, Matthew B.

doi:10.1038/s41467-024-46109-x

Title: Viral potential to modulate microbial methane metabolism varies by habitat

Journal Article · 29 February 2024 · Nature Communications

DOI: https://doi.org/10.1038/s41467-024-46109-x · OSTI ID:2471120

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Ohio State University, Columbus, OH (United States)
Cornell University, Ithaca, NY (United States); Ohio State University, Columbus, OH (United States)
Wageningen University and Research (The Netherlands); University of Vienna (Austria)
University of Vienna (Austria)
Ruđer Bošković Institute, Zagreb (Croatia); Center of Excellence for Science and Technology-Integration of Mediterranean Region, Zagreb (Croatia)

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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: Gordon and Betty Moore Foundation; National Science Foundation (NSF); USDOE

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830

OSTI ID:: 2471120

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Viral potential to modulate microbial methane metabolism varies by habitat

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