Vegetation increases CH ₄ emissions and methanotroph diversity in marine sediments

Abstract Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH₄) emissions, whose microbial and environmental descriptors in Zostera noltei meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH₄ fluxes, CH₄-producing and consuming microbial communities and sediment physico-chemical parameters in Z. noltei meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH₄ fluxes were measured at low tide and microbial communities were characterised using targeted metagenomics of three functional genes ( mcrA, mmoX, pmoA ) and quantitative PCR. CH₄ fluxes were higher in vegetated than bare sediments (24.4 ± 2.6 vs. 9.4 ± 0.7 µmol m⁻² d⁻¹). Mixed linear models and random forest analyses identified C accumulation rate and CO₂ flux as the strongest positive descriptors of CH₄ fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera ( mcrA–Methanolobus, mmoX–Methylocella, pmoA–Methylococcus, Methyloglobulus ) emerged as abundant, seagrass-associated, correlated with CH₄ fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH₄ fluxes than gene abundance or a specific genus. Findings indicate Z. noltei meadows enhance C burial and CH₄ emission, with methanotroph diversity potentially mitigating CH₄ emissions. Our results provide the first integrated assessment of CH₄ fluxes and their descriptors in Z. noltei meadows, highlighting the intertwined nature of C burial and CH₄ emissions and the need to account for both in blue C climate assessments.