Paphia undulata enhances sedimentary CH₄ and N₂O emissions via divergent microbial mechanisms

Global aquaculture expansion has elevated its contribution to greenhouse gas (GHG) emissions, yet shellfish aquaculture's role in methane (CH₄) and nitrous oxide (N₂O) fluxes remains poorly understood due to conflicting findings and unclear mechanistic links between metabolic and bioturbation effects. This study employed a controlled laboratory experiment with Paphia undulata to isolate the impacts of metabolism and bioturbation on sedimentary GHG emissions, combining physicochemical monitoring, microbial community sequencing, and functional gene quantification. Results showed that suspended P. undulata (metabolism-only effect) increased mean N₂O flux by 60.07% via enrichment of Candidatus Nitrosopumilus, which triggered nitrification stalling at the nitrite stage and subsequent nitrifier denitrification. Buried P. undulata (combined metabolism and bioturbation) elevated mean CH₄ flux by 64.97% by enriching methylotrophic methanogen Methanococcoides and activating the methyl-disproportionation methanogenesis pathway, while ammonium excretion suppressed methanotrophic activity (reduced pmoA gene abundance). These findings demonstrate that P. undulata drives divergent GHG emission pathways through distinct microbial mechanisms, highlighting the necessity of integrating CH₄ and N₂O emissions into shellfish aquaculture's climate impact assessment and optimizing low-carbon farming practices.