Microbial oxidation significantly reduces methane export from global groundwaters.

Methane is ubiquitous in groundwater, and its release to surface environments through pumping, discharge, or diffusion is an emerging environmental concern. Microbial oxidation consumes methane and mitigates its release, but quantitative constraints in groundwater remain unknown. Using ultra-low-level 14C-labeling, we estimate in situ microbial methane oxidation rates in shallow carbonate and sandy aquifers from central and northern Germany with methane concentrations spanning 5 orders of magnitude, from 0.15 ± 0.04 to 36,250 ± 1,390 µg L-1. Oxidation rates ranged from 0.001 ± 0.0003 to 74.28 ± 46.94 µgC L-1 d-1 and were highly correlated with groundwater methane concentrations. Oxidation-based methane turnover was rapid at low methane concentrations, with complete consumption requiring days to weeks. In contrast, microbial oxidation at high methane sites required months to decades for complete methane turnover, indicating the potential for unconsumed methane to leak into local streams or wetlands. High oxidation rates were associated with gammaproteobacterial methanotrophs that typically thrive in suboxic conditions and anaerobic methane-oxidizing archaea, while uncultivated methanotrophs of the Methylomirabilota and Verrucomicrobiota dominated low-rate sites. Based on globally distributed groundwater methane concentration data, we extrapolated the strong observed correlation between methane concentrations and oxidation rates to global groundwater volumes, estimating that microbial oxidation removes ~66% of groundwater methane globally, equivalent to 167 to 778 Tg CH4 y-1. This highlights the groundwater microbiome as a crucial subsurface methane filter that reduces methane release to surface waters, soils, and the atmosphere.