Core structural shifts in procaryotic and fungal rhizosphere biomes of barley subjected to early waterlogging

Climate change is exacerbating rainfall events, leading to higher flood risks and significant threats to soil biodiversity. Yet the response of plant-associated fungi and bacteria to the effects of extreme rainfall in cropland remains poorly understood. Here, we investigated the effects of one, experimentally created, intense event of waterlogging at the start of the growing season on the structure of rhizosphere bacterial and fungal communities across a diverse set of ten barley genotypes. We used 16S rRNA and ITS-based amplicon sequencing to profile the microbial communities. Waterlogging, experimentally imposed in the field at the start of the season, majorly altered the structure of microbial assemblages in the rhizosphere across barley genotypes offering very clear evidence that, beyond possible differences due to genotypes, the barley core microbiome consistently responded to this single perturbation. Functional annotations of the amplicon sequencing data allowed formulating the hypothesis that shift in the abundance of specific fungal and bacterial genera could mitigate the impact of water stress. Future studies should concentrate on validating and teasing apart the functional implications of the observed changes with dedicated measurements and aim at characterising the specific response of different genotypes, which will help understanding the resistance and resilience of soil and crops to waterlogging stress.