Dynamic changes in root exudate profile under waterlogging and interactions with rhizosphere microbial community in rapeseed

Environmental stresses alter root exudate profile, modulating rhizosphere microbial communities. Yet the impacts of waterlogging on root exudates and how their dynamics shape the rapeseed rhizosphere microbiome remain unknown. This study aimed to investigate the effects of waterlogging on the dynamics of root exudates and their correlations with rhizosphere microbial communities. In this pot experiment, untargeted LC–MS/MS-based metabolomics analysis was performed using a Thermo Fisher UHPLC-Exploris 240 system to identify root exudates. Furthermore, Soil microbial communities were analyzed using techniques such as next-generation sequencing (NGS) of the 16S rDNA gene for the bacterial community and internal transcribed spacer (ITS) for the fungal community. A total of 4838 root exudate metabolites were identified. Waterlogging significantly altered the root exudate profile, with differentially expressed metabolites (DEMs) mainly involved in amino acid metabolism, phenylpropanoid biosynthesis, the TCA cycle, biosynthesis of various plant secondary metabolites, ABC transporters, and galactose metabolism. It also significantly reshaped rhizobacterial and rhizofungal community composition and diversity. Key induced DEMs under waterlogging were identified. Root exudates exhibited significant correlations with rhizobacterial and rhizofungal phyla, genera, and diversity indices, implying that they play a crucial role in waterlogging tolerance. Notably, key DEMs (e.g., gamma-aminobutyric acid, abscisic acid, melatonin; 3-methylsalicylic acid, scopoletin, hesperetin, and niazirin) were significantly positively correlated with plant growth-promoting microbial species, including Rhizobium , Pseudomonas , and Clostridium_sensu_stricto_1 . Our findings demonstrate that root exudates play a crucial role in mediating waterlogging tolerance by facilitating the recruitment of beneficial microbial species.