Increasing natural emissions of the greenhouse gas methane (CH₄) substantially impact the Earth climate. In this context, near-shore waters play a key role because water column CH₄ concentrations in these areas are much higher when compared with the open waters. However, little is known about CH₄ emitters in shallow coastal zones or their contribution to the atmospheric CH₄ flux. Moreover, a series of recent studies indicate that microbial CH₄ production is not limited to strictly anoxic conditions and might be widespread in the oxic water column. This oxic CH₄ production places the CH₄ source close to the water surface, thereby intensifying fluxes to the atmosphere. Based on these recent investigations and a proposed linkage between primary production and CH₄ formation, we hypothesize that microphytobenthos (MPB) communities, as major primary producer in many coastal systems, play a significant role in shallow-water CH₄ dynamics. To explore MPB-associated CH₄ production, we will investigate the potential of this CH₄ source, by conducting incubation experiments and determining the rates of both primary production and CH₄ production by abundant benthic diatom species. The use of a novel cavity ring-down spectroscopy-based semi-continuous method in closed incubation experiments will enable sensitive measurements of CH₄ production in high temporal resolution over day/night cycles. The experiments will be undertaken under controlled temperature and light conditions and will use axenic/xenic clonal cultures of selected MPB diatoms to identify the main effectors and those species with the highest CH₄ production rates. Experiments using ¹³C-labeled precursor substrates will be performed to identify and characterize MPB-associated CH₄ production pathways. Previous studies of oxic CH₄ production were mostly mechanistic laboratory studies that used culture samples; whether the measured CH₄ production rates were representative of those in natural systems was not determined. To overcome these limitations in our study, the incubation experiments with clonal cultures will be accompanied by natural MPB communities sampled from the shallow waters at Askö island (Swedish Baltic Sea) and from the inner coastal waters of the Darss-Zingst Bodden Chain (German Baltic Sea), thus covering different sediment types, hydrodynamic conditions, and MPB communities. To align benthic CH₄ fluxes from MPB communities with overall benthic and sea-to-air fluxes of CH₄, we will determine CH₄ fluxes between the sediment, water column, and atmosphere in both study areas.