Soil microbial communities in Danish lowlands are shaped by soil pH

Agricultural activity on drained lowlands is a common practice in Denmark and there are suggestions to rewet some of them for climate mitigation purposes. Rewetting those lowlands might result in a change in microbial community composition. This study investigates the current prokaryotic diversity and community composition in soil samples from cultivated lowlands to provide the baseline for monitoring changes after rewetting. Furthermore, variations in soil properties between sites are examined, and the properties driving differences in prokaryotic diversity and community composition are identified. In total, 116 samples were collected from field sites across Denmark that were categorized as one of four different land-use types: Crop, Grass, Fallow, and Other. Soil properties were selected to cover chemical (soil water repellency, pH, electrical conductivity), hydrological (depth to ground-water table, soil water content at field capacity (-100 hPa)), nutrient-related (total nitrogen, organic carbon, carbon-to-nitrogen-ratio, fractions of pyrolizable and residual organic matter), and structural (total porosity, pore size distribution index) functions of the soil. Soil samples exhibited significant variations in their chemical and physical properties, including pH ranging from 2.02 to 7.55, organic carbon ranging from 3 g 100g^-1 to 50 g 100g^-1, soil water repellency ranging from 71.27 mN m^-1 (hydrophilic) to 33.85 mN m^-1 (very strongly hydrophobic), and total porosity ranging from 51% to 95%. Soil samples clustered according to soil class (mineral, organo-mineral, organic, highly organic) but not according to land-use type (crop, grass, fallow, other). Prokaryotic alpha diversity, measured as Shannon’s diversity index (H), ranged from 4.16 to 5.89 across samples and could best be predicted by pH, followed by total porosity, fraction of pyrolizable carbon, and pore size distribution index. The pH alone explained 36% of the variation in H between samples. Hierarchical clustering identified three prokaryotic clusters highly correlated with pH. A weak correlation was found between differences in community composition (beta diversity) and geographic distance (r = 0.15, p < 0.001). However, pH was also the main driver of beta diversity, explaining 11% of the variation. At the same time, models including additional variables only had marginally better explanatory power. In conclusion, pH was the predominant driver of prokaryotic alpha and beta diversity across land-use types in lowland soils.