loading . . . Soil bacteria and fungi diversity analysis reveals effects of sesame (Sesamum indicum L.) under waterlogging stress - BMC Microbiology Background Sesame is one of the major drought-tolerant oil crops, but its growth and development, soil properties and microbial diversity are susceptible to waterlogging stress, affecting overall sesame yield. However, the Changes in microbial communities and the interactions under waterlogging stress in sesame have not been documented. To address this gap, we investigate the effect of waterlogging stress on soil chemical properties in two sesame varieties at the onset flowering stage. Subsequently, the compositions and diversity of soil microbial communities were analyzed by using bacterial 16 S rRNA and fungal ITS sequencing methods (n = 5). Results In this study, 44,820 bacterial and 2,005 fungal operational taxonomic units were obtained and assigned to 33 bacterial and 16 fungal phyla, respectively. Proteobacteria and Firmicutes tended to be found more under waterlogging stress than normal watering stress. Soil bacterial communities primarily comprised Proteobacteria, Firmicutes, Actinobacteriota and Acidobacteriota, and the soil fungal community was dominated by Ascomycota, Mortierellomycota, Glomeromycota and Basidiomycota. Under waterlogging stress condition, the abundance of Firmicutes and Basidiomycota increased, while Actinobacteriota, Acidobacteriota, Mortierellomycota and Glomeromycota decreased. In the waterlogging-sensitive line SP, the relative abundance of beneficial bacterial genus Pseudomonas was increased under waterlogging stress. Alpha diversity analysis revealed that waterlogging stress had a significantly effect on the ACE, PD-tree and Shannon indexes of bacterial and fungal communities in the soil. While beta diversity analysis indicated that there were significant differences in bacterial and fungal communities in two sesame varieties under waterlogging stress. In addition, waterlogging stress had significant (p < 0.05) effects on soil pH, AP (Available Phosphorus) and AK (Available Potassium) in two sesame varieties. Redundancy analysis results revealed that the correlation between soil pH and AP with soil microbial communities was significantly stronger than that with other factors, and they are the main environmental factors affecting changes in soil structure and microbial communities. Conclusions By systematically investigating the effects of waterlogging stress on the community structure, diversity, and key driving factors of sesame rhizosphere microorganisms, this study not only clarified the response characteristics of dominant rhizosphere microbial groups under waterlogging conditions (such as changes in the relative abundance of specific beneficial bacterial genera) but also revealed the mechanism underlying the association between soil physicochemical properties (e.g., pH, available phosphorus) and microbial community dynamics. This lays a solid core foundation for subsequent in-depth research on the dynamic change patterns of sesame rhizosphere microorganisms. https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04371-z
