Vegetation Increases CH₄ Emissions and Methanotroph Diversity in Marine Sediments

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 noltii meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH₄ fluxes, CH₄-producing and consuming microbial communities and sediment physicochemical parameters in Z. noltii meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH₄ fluxes were measured at low tide during daytime conditions, providing standardized estimates of peak emissions. Microbial communities were characterized 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 day^-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. noltii 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. noltii meadows, based on limited temporal coverage capturing the daytime peak emission conditions, highlighting the intertwined nature of C burial and CH₄ emissions and the need to account for both in blue C climate assessments.