Responses of an Agricultural Soil Microbiome to Flooding with Seawater after Managed Coastal Realignment

Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with seawater. How flooding with seawater impacts soil microbiomes and the biogeochemical cycling of elements is poorly understood. To address this, we conducted a microcosm experiment using soil cores collected at the nature restoration project site Gyldensteen Strand (Denmark), which were flooded with seawater and monitored over six months. Throughout the experiment, biogeochemical analyses, microbial community fingerprinting and the quantification of marker genes documented clear shifts in microbiome composition and activity. The flooding with seawater initially resulted in accelerated heterotrophic activity that entailed high ammonium production and net removal of nitrogen from the system, also demonstrated by a concurrent increase in the abundances of marker genes for ammonium oxidation and denitrification. Due to the depletion of labile soil organic matter, microbial activity decreased after approximately four months. The event of flooding caused the largest shifts in microbiome composition with the availability of labile organic matter subsequently being the most important driver for the succession in microbiome composition in soils flooded with seawater.