Freshwater ecosystems are an important source of the greenhouse gas methane (CH₄), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH₄ emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH₄ emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH₄ fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH₄ emissions, while dredging showed a trend towards decreasing CH₄ emissions. Total CH₄ emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH₄ emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH₄⁺ concentrations, lowering CH₄ production rates. Second, dredging decreased CH₄ emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH₄⁺ and O₂, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH₄ emissions, mitigating climate change.

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