Advection and diffusion determine vertical distribution of microbial communities in intertidal sediments as revealed by combined biogeochemical and molecular biological analysis

Porewater advection stimulates nutrient exchange and microbial activity in shallow marine sediments, whereas element cycling in deeper diffusion-dominated sediments is comparatively slow due to limited nutrient supply. We studied the vertical distribution of microbial communities and organic matter (OM) cycling in these contrasting porewater regimes down to 5 m depth at an intertidal flat of the southern North Sea. Archaea, Bacteria and Eukarya were targeted, combining intact polar lipid (IPL) analysis with qualitative and quantitative molecular biological techniques. The largely sandy section 1 of the core (50 cm) and the diffusion-dominated section 2 (75–490 cm). This suggests bacteria adapting their membranes in response to increasing physicochemical stress and starvation in the nutrient limited, fine grained sediments of section 2 with less bioavailable, predominantly terrestrial, OM. Relative amounts of bacterial acyl ether and diether phospholipids increased in this lower section and were assigned to sulfate reducers and yet uncultured myxobacteria. Archaea were an order of magnitude less abundant than Bacteria, and were affiliated mainly with Methanosarcinales and Methanomicrobiales. Accordingly, the archaeal IPL composition was typical for a methanogenic community. IPLs not exclusively derived from in situ microbial production emphasize that these biomarkers have to be interpreted with caution in sediments with complex hydrogeology. Our results demonstrate that contrasting subsurface flow regimes significantly impact on the vertical zonation of biogeochemical properties and microorganisms in marine sediments