Viral modulation of microbial methane production and oxidation varies by habitat

Zhong, Zhi-Ping; Du, Jingjie; Köstlbacher, Stephan; Pjevac, Petra; Orlić, Sandi; Sullivan, Matthew (2024) Viral modulation of microbial methane production and oxidation varies by habitat. Nature Communications, 15 . ISSN 2041-1723

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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.

Item Type:	Article
Uncontrolled Keywords:	methane; virus; AMG
Subjects:	NATURAL SCIENCES > Biology NATURAL SCIENCES > Biology > Microbiology
Divisions:	Division of Materials Chemistry
Projects:	Project title Project leader Project code Project type Mikrobna ekologija jezerskih ekosutava - novi pristup-MALENA Sandi Orlić IP-2020-02-9021 HRZZ Razvoj testa na osnovi nukleinskih kiselina za identifikaciju vrsta koje ukazuju na kvalitetu vode- Sandi Orlić KK.01.2.1.02.0335 EK STIM-REI-STIM-REI Vlasta Bonačić-Koutecky; Tvrtko Smital; Sandi Orlić; Ante Bilušić; Mile Dželalija; Damir Kovačić; Darko Koračin; Željka Sanader Maršić KK.01.1.1.01.0003 EK
Depositing User:	Sandi Orlić
Date Deposited:	25 Nov 2025 08:58
URI:	http://fulir.irb.hr/id/eprint/10221
DOI:	10.1038/s41467-024-46109-x

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