Root exudate redox dynamics under flooding: emerging insights into rhizosphere microbial interactions and plant–soil responses

Flooding and waterlogging increasingly disrupt plant-soil interactions by reshaping the rhizosphere through interconnected biophysical, chemical, and biological processes. Oxygen depletion under flooded conditions rapidly creates hypoxic to anoxic environments, which induce shifts in root physiology, anaerobic metabolism, and root exudation. Metabolites detected in roots or xylem sap represent distinct metabolic or transport processes and should be differentiated from compounds identified as root exudates. The increased release of fermentation products reshapes rhizosphere chemistry and microbial community assembly. Flood-induced redox changes promote a transition from aerobic to anaerobic microbial communities, favoring denitrifiers, iron and sulfate reducers, and methanogens, with significant consequences for nutrient cycling and greenhouse gas emissions. Plant-growth promoting rhizobacteria (PGPR) can mitigate flooding stress through mechanisms such as ACC deaminase activity and antioxidant regulation; however, their effectiveness is often constrained under fluctuating redox conditions, highlighting the potential for microbial consortia. The post-flood re-aeration phase is a critical but understudied period during which shifts in root metabolism and exudation regulate rhizosphere recovery and microbial reassembly. The flooding-to-re-aeration transition involves dynamic redox changes affecting root metabolism, exudation, microbial functions, and rhizosphere recovery. Concepts such as plant stress memory and microbiome legacy further highlight the long-term impacts of flooding. This review synthesizes insights from plant physiology, microbial ecology, and metabolomics to characterize rhizosphere responses to flooding, focusing on oxygen dynamics, redox shifts, and exudate-mediated microbial restructuring. It also identifies key knowledge gaps and outlines future research directions to enhance crop resilience through microbiome-based strategies. Overall, plant resilience depends on coordinated plant-microbiome interactions. Integrative approaches combining metabolomics and microbial community profiling are needed to improve crop performance under flood conditions.