Coupling methane oxidation to pollutant transformation: a microbiome framework for climate mitigation and soil remediation

Methane emissions and chemical pollutants often co-occur in natural and engineered environments, contributing to ecosystem degradation. Microorganisms play key roles in regulating these processes through methane oxidation and pollutant transformation, thereby linking greenhouse gas dynamics with contaminant fate and risk across soils and aquatic systems. In this review, we summarize current knowledge on microbial species (methanotrophs) involved in methane oxidation and the transformation of metal(loid)s (As, Cr, V, Sb and Hg) and organic pollutants (trichloroethylene, sulfamethoxazole, and PAHs), with a focus on both aerobic and anaerobic pathways in environmental and engineered systems. We examine how methane oxidation is coupled to pollutant transformation through direct enzymatic reactions carried out by methanotrophs, as well as through indirect pathways involving electron transfer and intermediates released from methane oxidation. Depending on pollutant types and redox conditions, these couplings can result in contrasting outcomes, with different toxicity and mobility. Building upon this understanding, we propose a conceptual framework to guide microbiome-based strategies for concurrent mitigation of methane emissions and risks from metal and organic pollutants in soils and aquatic systems. The framework integrates site-specific characterization of pollutant profiles and microbial communities, including aerobic and anaerobic methanotrophs and associated pollutant-transforming microorganisms, with targeted manipulation of microbial consortia through top-down and bottom-up approaches, together with monitoring of key biogeochemical indicators to support context-dependent decision-making. By linking process-level coupling mechanisms with decision-oriented microbiome strategies, this framework provides a structured basis for evaluating when and how methane-related microbial processes can be harnessed for concurrent climate mitigation and soil remediation under site-specific redox and contamination conditions.