Microbes play an important role in mediating biogeochemical cycles. Understanding the ecological interactions driving the activity of these microbes is particularly important for methane (CH4) dynamics, a powerful greenhouse gas. Shallow inshore waters are hotspots for CH4 emissions from marine systems, but it is still unclear what are the dominant ecological factors explaining such high emissions. In sediments, methane oxidizing bacteria (so called methanotrophs) function as an important ‘benthic filter’ by removing CH4 and thus modulating the sediment-to-water flux. The overarching goal of this project is to understand to what extent methanotrophy in the sediment surface modulates CH4 emissions from shallow coastal areas. Sediment samples were collected on research vessel Augusta from 8 stations along a water depth gradient (5–30 m water depth) in the Pemarfjärden estuary located on the south-east coast of Finland (2nd week of September 2021). The sampling cruise consisted of a consortium of different scientists from Tvärminne Zoological Station and Stockholm University in the so called “Baltic Bridge” collaboration (Alf Norkko, Tom Jilbert, Christoph Humborg, Anna Villnäs, Florian Roth). Numerous different field variables were measured (e.g. salinity, temperature, water depth), benthic macrofauna, CH4 water and air concentrations, and water plus sediment chemistry such as CH4 pore-water profiles and C and N isotopes to estimate the origin of the organic matter (e.g. terrestrial or marine). Surface water and air concentrations of CH4 were measured with a Water Equilibration Gas Analyser System (WEGAS) as outlined in Humborg, Geibel, Sun, McCrackin, Mörth, Stranne, Jakobsson, Gustafsson, Sokolov, Norkko and Norkko. Considering that benthic aerobic methanotrophs reside in the aerated sediment surface, the 0.0-0.5 cm and 0.5-1.0 cm layers were sliced starting from the sediment surface. The slices were homogenized, and sub-sampled for DNA extraction. The DNA was extracted from the sediments using the DNeasy PowerSoil kit (Qiagen), and libraries prepared for sequencing at Stockholm University. The sequencing were done at SciLife, Stockholm with the Illumina NovaSeq 6000 that has previously been used with good results. The metagenome samples will make it possible to look for functional genes with a focus on genes involved in CH4 oxidation, and their relationship to geochemical variables in the sediment.