Sediment Core Sampling and Analysis

Three replicate sediment cores were sampled with a Kajak gravity corer at each location to give 24 acrylic cores (inner diameter: 7 cm; length: 60 cm) for each bay and a total of 48 cores per sampling occasion as described in Seidel et al. (2022 (link)). Surface plus bottom water temperatures and bottom water oxygen concentrations were measured in situ (Multiline™ sensor, WTW™) during sampling. Additionally, overlying bottom water samples (BW; 50 ml) were taken from the sediment (SED) cores close to the SED surface and transferred into sterile tubes (Thermo Scientific™) for 16S rRNA gene amplicon sequencing (described below). An additional 15 ml of BW was filtered through a 0.7-μm Target2™ GMF Syringe Filter (Thermo Scientific™) into a pre-acid washed polypropylene tube (Thermo Scientific™) for chemical analyses. The BW was decanted from the core, and a 0–1-cm SED slice was collected in a sterile 50-ml polypropylene tube (Thermo Scientific™). The tube contents were well-mixed, and 15 ml was transferred to a pre-acid washed polypropylene tube (Thermo Scientific™) for subsequent pore water analysis. A further 2-ml reaction tube (Sarstedt, Inc.) was filled with SED for organic matter (OM) analysis. All samples were cooled during transport to the laboratory on the same day where they were frozen at either −80 or −20°C.