Figure 3.

Main flood effects on plant endosphere microbiome, including the root system and the aerial part of the plant. Low oxygen (O₂) conditions induced by flooding impact the root microbiome by producing a switch from aerobic to anaerobic microorganisms. Alterations of the chemical composition of the root system due to the activated fermentative pathways, and the reduced growth of the root system due to hypoxia or ethylene synthesis, produced dysbiotic changes on the microbial community composition of the root system. These dysbiotic changes are usually produced by the increase in the competitive ability of certain microbes, i.e. oomycete pathogens or ethanol‐catabolizing microorganisms, and the inhibition of the presence of beneficial aerobes such as endophyte or mycorrhizal fungi. Variations on root system architecture may also cause adjustments in the root microbial community, with a probable reduction in the richness and diversity of species due to low nutrient provision. The extent to which new developed adventitious roots contribute to alterations on the root microbiome remains unknown. Furthermore, the signals generated on the root system, especially the diffusible ones such as ethylene or methane (CH₄), can affect the phyllosphere microbiome by inhibiting bacterial symbiosis or enhancing the presence of Methylobacterium, a bacterial genus with the ability to use CH₄ as a carbon source. Root adaptations induced by the synthesis and signalling of ethylene, such as adventitious roots, radial oxygen loss (ROL) barriers and aerenchyma attenuates flooding (hypoxic) stress on root microbial composition. Futhermore, the presence of certain microbes can improve flooding stress tolerance by enhancing aerenchyma formation (as in the case of the fungi Phomopsis liquidambari) or the development of ROL barriers (as in the case of certain anaerobic microbes). Microbes producing ACC‐deaminase can mitigate ethylene stress. Other endophytes, such as dark septate endophytes (DSE), can increase root growth by enhancing nutrient uptake and ameliorating the plant antioxidant response. Created with BioRender.com [Color figure can be viewed at wileyonlinelibrary.com]