Impacts of flooding on agricultural soil microbiome

As a result of climate change, increased flooding events have been recorded across the globe. The role of soil microbiomes in soil health and fertility is well recognized, as these microbial communities drive essential processes such as nutrient cycling, organic matter decomposition, and plant health. The composition and function of these communities can be highly sensitive to environmental changes. The aim of this study is to identify the impacts of flooding on soil microbiome composition and diversity. Paired flooded and non-flooded agricultural soils were collected from Germany, Ireland, and Portugal, and characterized using full-length 16S rRNA gene and ITS amplicon sequencing. Following false-discovery-rate correction, flooding was not associated with significant differences in bacterial or fungal alpha diversity. In contrast, paired PERMANOVA detected small overall effects of flooding on bacterial Bray-Curtis, Jaccard, and unweighted UniFrac distances, and on fungal Bray-Curtis and Jaccard distances, although community composition was structured more strongly by country. At the taxonomic level, Thermodesulfobacteriota was more highly represented in flooded soils, whereas the fungal phyla Ascomycota and Mortierellomycota were less represented. Eight bacterial genus-level assignments differed between conditions after correction, whereas no fungal genus-level differences remained significant. Flooding was associated with some geographically dependent restructuring of bacterial and fungal communities rather than a consistent loss of microbial diversity. These findings demonstrate the importance of regional context when evaluating microbiome responses to flooding and identify the need for future studies that integrate microbial data with measured soil physicochemical characteristics.IMPORTANCEFlooding is an increasingly important disturbance in agricultural soils, yet its effects on bacterial and fungal communities remain incompletely understood. By comparing matched flooded and non-flooded soils across Germany, Ireland, and Portugal, this study shows that flooding was associated with small shifts in community composition without a consistent reduction in alpha diversity. Geographic location explained the dominant patterns in community structure, while a limited number of bacterial and fungal taxa differed between flooding conditions. These findings indicate that microbiome responses to flooding are context-dependent and are expressed primarily as changes in community composition rather than uniform losses of richness or evenness. The study provides a cross-country baseline for future work linking flood-associated microbial changes to measured soil chemistry, flooding history, and agricultural recovery.