Impact of Flooding on Agricultural Soil Microbiome Composition and Diversity.

According to the World Health Organisation, climate change represents one of the most significant threats to global health. 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-recognised, 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. Soil samples were taken from a total of 23 flooded and 23 non-flooded sites across Ireland, Germany and Portugal. DNA was extracted from all samples and extensive quality control procedures were performed. Long-read ITS and 16s rRNA amplicon sequencing using PacBio technology were performed on the same samples. In-depth bioinformatic analysis performed on the sequenced data revealed a decrease in the number of bacterial amplicon sequence variants (ASVs) in flooded soils compared to non-flooded, which highlighted a reduction in microbial richness. Several beneficial bacteria, some of which include Nitrospira, Acidothermus, Pseudomonas and Bradyrhizobium, were decreased ion flooded soil. In flooded soils, many beneficial fungal genera were found to be decreased or missing, some of which include Chaetomium, Sebacina, Chrysosporium and Penicillium. This decrease in beneficial bacteria and fungi due to flooding may impact soil health and fertility and factors that lead to a more or less resilient soil microbial community need to be investigated as we experience more frequent and intense flooding events.