Figure 5.

Main direct and indirect flood effects experienced by the plant and its associated microbiome. Direct effects of flooding on the plant and the plant microbiome are mainly driven by hypoxic soil conditions. Flooding changes the normal plant aerobic metabolism into a fermentative metabolism involving enhanced carbohydrate consumption through glycolysis. A hormonal imbalance due to increase ethylene synthesis also occurs, leading to different detrimental processes in the plants such as the inhibition of photosynthesis. Plant physiological and metabolic alterations drive the plant‐associated microbiome (including the rhizosphere and the endosphere microbiome). These changes include modifications in xylem sap pH, alterations on the chemical composition of root tissues or root exudates due to the production of ethanol during fermentation or changes on carbohydrate content, which usually lead to negative microbial recruitments. Nevertheless, the root exudation of specific chemical components may enhance the recruitment of certain microbes that counteract some negative stress effects (“cry‐for‐help” mechanism). Alterations on the root system architecture (RSA), e.g., reflected in reduced root growth, can alter the plant microbiome diversity; the development of new adventitious roots has an unknown effect on microbial composition. On the other hand, hypoxic soil conditions induced by flooding promote the enrichment of anaerobic microbes, which are usually linked with processes such as fermentation, methanogenesis or denitrification. The presence of these microorganisms produces indirect negative effects on the plant, such as soil denitrification or the outcompetition of certain microbial members by others with pathogenic behaviour. Nevertheless, the persistence of some microbes under stress conditions may have beneficial effects for the plant during the stress. For example, the establishment of endophytes such as the dark septate endophytes (DSE) or the endophytic fungi Phomopsis liquidambari may be involved in enhancing root growth, by improving nutrient uptake, or in stimulating the formation of aerenchyma. Other symbiotic microbes such as the plant‐growth promoting rhizobacteria (PGPR) are able to synthesise the enzyme ACC‐deaminase that cleaves ACC and reduces ethylene synthesis. Created with BioRender.com