Methane dynamics along the salinity gradient of the Scheldt estuary

Abstract. Estuaries are important natural sources of methane (CH₄) to the atmosphere. These transitional aquatic systems connect freshwater, brackish and fully marine environments. The pronounced salinity gradient, characteristic of estuaries, impose particular challenges to microbes and influence the biogeochemical processes they mediate. Salinity changes can inhibit methanotrophic activity. Here we analysed methane dynamics and microbial communities in the estuary of the Scheldt River, which flows through northern France, western Belgium, and the southwestern Netherlands, and finally discharges into the North Sea. During a research cruise conducted in June 2022 from the river mouth to Antwerp, water samples were collected at ten stations along the estuarine salinity gradient. We investigated water column CH₄ inventory and stable carbon isotope dynamics, together with methane oxidation rates. Elevated CH₄ concentrations of up to 110 nM with associated δ¹³C -values of about −46 ‰ were found in the freshwater zone of the upper estuary (in the area of the city of Antwerp). Rather than a gradual decrease in CH₄ towards the North Sea, we observed a second maximum of 180 nM in the marine zone, with a contrasting isotopic composition of -66 ‰ indicating distinct methanogenic pathways and/or substrates in the estuary. Methane oxidation rates showed no clear relationship with the salinity gradient. In contrast, the composition of the methanotrophic community shifted markedly along the estuary and the salinity gradient, with Methyloparacoccus and Crenothrix prevailing in the freshwater zone Methyloceanibacter and PLTB-vmat-59 dominating in the mixing and marine zones. Our results thus demonstrate that the salinity gradient is not the primary control on estuarine methane oxidation capacity but the community composition of the methane oxidizing bacteria (MOB). In sediments, the MOB community composition mirrored the patterns observed in the overlying water column, indicating that estuarine sediments represent both a key habitat and an important recruitment source sustaining methanotrophic communities in the water column. Despite an active microbial filter, methane oxidation accounted for only a minor fraction of the estuaries’ CH₄ budget. Most methane (about 98 %) was lost through advection and diffusive fluxes to the atmosphere, while a smaller fraction was exported to the North Sea, contributing to sustained methane supersaturation in coastal waters.