Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.

Benthic microbial communities of intertidal zones perform important biogeochemical processes and provide accessible nutrients for higher organisms. To unravel the ecosystem services of salt marsh microbial communities, we analyzed bacterial diversity and metabolic potential along the land–sea transition zone on seasonal scales on the German North Sea Island of Spiekeroog. Analysis of bacterial community was based on amplicon sequencing of 16S rRNA genes and –transcripts. Insights into potential community function were obtained by applying the gene prediction tool tax4fun2. We found that spatial variation of community composition was greater than seasonal variations. Alphaproteobacteria (15%), Gammaproteobacteria (17%) and Planctomycetes (11%) were the most abundant phyla across all samples. Differences between the DNA-based resident and RNA-based active communities were most pronounced within the Planctomycetes (17% and 5%) and Cyanobacteriia (3% and 12%). Seasonal differences were seen in higher abundance of Gammaproteobacteria in March 2015 (25%) and a cyanobacterial summer bloom, accounting for up to 70% of the active community. Taxonomy-based prediction of function showed increasing potentials for nitrification, assimilatory nitrate and sulfate reduction from sea to land, while the denitrification and dissimilatory sulfate reduction increased towards the sea. In conclusion, seasonal differences mainly occurred by blooming of individual taxa, while the overall community composition strongly corresponded to locations. Shifts in their metabolism could drive the salt marsh’s function, e.g., as a potential nitrogen sink.