The primary consequence of flooding is the exposure of plants to an oxygen-deprived environment. In response to anoxic conditions, plants promptly enhance carbohydrate metabolism through glycolysis for energy production (Zou et al., 2010; Butsayawarapat et al., 2019; Kaur et al., 2021). Waterlogging-induced up-regulation of PDC, alcohol dehydrogenase (ADH), and sucrose synthase (SUS) genes, which are associated with sucrose synthase, glycolysis, and fermentation pathways. However, after the waterlogging waters receded, the expression levels of these genes decreased (Zhao et al., 2018). Furthermore, the activity of glycolytic enzymes is also affected. Hypoxia induces a shift in sugar metabolism and inhibits the tricarboxylic acid cycle, leading to increased glycolytic flux and accumulation of succinate in grapevine roots (Ruperti et al., 2019). A similar response is observed in cucumbers and cruciferous species. Transcriptomic analysis of root systems from various species revealed that flooding induces the activation of genes associated with glycolysis, facilitating energy release under different durations of inundation. Additionally, we noted a positive correlation between early upregulation of glycolytic genes and enhanced flooding tolerance. Conversely, varieties exhibiting poor waterlogging tolerance exhibited delayed regulation of glycolysis-related genes (Hwang et al., 2020; Kęska et al., 2021).

Amino acid metabolism plays a pivotal role in response to flooding stress. Under waterlogging conditions, cucumber root system regulates gene expression related to amino acids, including the degradation pathways of valine, leucine, and isoleucine. Concurrently, lactic acid accumulation increases during hypoxic stress caused by waterlogging, resulting in a decrease in cytoplasmic pH. Aspartate transferase and glutamate decarboxylase, integral components of amino acid metabolism, play a crucial role in regulating the cytoplasmic pH value of cucumber plants (Kęska et al., 2021). Grape roots exposed to low oxygen levels caused by flooding exhibit overexpression of numerous genes involved in amino acid metabolism (Ruperti et al., 2019). Furthermore, waterlogging-induced stress upregulates glutathione peroxidase (GPX) and glutathione S-transferases (GST) genes in alfalfa plants, thereby activating pathways associated with amino acid metabolism such as amino sugar and nucleotide sugar metabolism as well as arginine and proline metabolism (Zeng et al., 2019).

Flooding can significantly increase the level of ROS in plants and destroy the homeostasis of ROS. In response to damages caused by ROS, plants promptly upregulate genes encoding ROS scavenger enzymes, like catalase, to mitigate ROS levels early while safeguarding cells from death (Raza et al., 2021). Furthermore, phenylpropanoid biosynthesis pathway, which plays a crucial role in tolerance to various oxidative stresses in plants, was notably enriched in waterlogging-resistant varieties of the same plant species under waterlogging stress (Wang et al., 2021a). The expression of transcription factors and genes associated with the ROS signaling pathway was found to be lower in less tolerant varieties, suggesting that enhancing ROS scavenging enzyme activity and reducing ROS accumulation could potentially enhance plant tolerance to waterlogging stress. Additionally, increased ROS scavenging enzyme activity during reoxygenation after waterlogging has been observed in both monocotyledonous and dicotyledonous plants, aiding their ability to cope with reoxygenation-induced damage and adapt to changing environmental conditions (Yuan et al., 2017; Zhao et al., 2018; Yu et al., 2020).

Meanwhile, the synthesis of specific secondary metabolites, such as lipids and hormones, significantly contributes to plant stress response, including flooding. For instance, in cucumber, esterase/lipase genes were strongly upregulated under waterlogging, suggested enhanced lipid metabolism with tolerance to waterlogging (Kęska et al., 2021).

The expression of transcription factors associated with hormonal responses, particularly ethylene, exhibited significant alterations during flooding stress. Ethylene is a key hormone in plant germination, differentiation, flowering and fruiting (Dubois et al., 2018), and oxygen induction is controlled by ethylene signaling under hypoxic conditions. The ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized in the roots of plants and subsequently transported to the stem through the xylem, thus mediating plant flooding tolerance. Increased expression of ERFs and ethylene synthesis-related genes was observed in plants such as Arabidopsis, chrysanthemum, sesame and corn during waterlogging events (Wang et al., 2016; Yeung et al., 2018; Zhao et al., 2018; Dossa et al., 2019; Yu et al., 2019, 2020). Additionally, regulation of auxin signals also plays a crucial role by modulating germ elongation and development, secondary metabolism, carbohydrate metabolism, and mitochondrial electron transfer, under submerged conditions in rice (Wu and Yang, 2020). JA also participates in multiple aspects of the plant recovery phase. It primarily regulates beneficial rhizosphere bacteria-triggered induced systemic resistance, thereby playing a pivotal role in defense responses. Pterocarya stenoptera enhances waterlogging tolerance by increasing the synthesis of methyl linolenic acid and flavonoids, while activating JA signaling pathways (Li et al., 2021). In A. thaliana and rice, JA restricts root growth to minimize energy consumption under submergence conditions (Chen et al., 2019; Shukla et al., 2020). In Arabidopsis, ABA may also influence recovery from flooding stress through interaction with ethylene (Yeung et al., 2018).

Flooding can directly induce plant hypoxia, disrupting the energy balance within plant and perturbing the equilibrium of ROS production and scavenging. In rice, it was observed that under submerged conditions, electron transfer in mitochondria and chloroplasts was impaired, leading to inhibition of photosynthetic rate and reduction in cellular energy charge, consequently resulting in ROS accumulation. There was an upregulation of ROS scavenging protein (peroxidase), which led to a decrease in MDA content and O₂- formation rate, while activating the antioxidant system to regulate ROS scavenging pathways in order to maintain the equilibrium of ROS at non-toxic level (Xiong et al., 2019). Peroxidase also plays a crucial role in safeguarding plant cell membranes, facilitating aerenchyma formation, and modulating cell wall remodeling in Maize (Hofmann et al., 2020). In the investigation on Kandelia candel Druce, a highly flooding resistant plant, flooding triggered an elevation in leaf ROS levels that phosphorylated serine/threonine protein kinases and activated MAPKs recognizing these phosphorylation sites (Pan et al., 2018). This mechanism is also present in Arabidopsis thaliana. Flooding leads to increased ROS levels prompting the activation of MAPK6 for enhanced survival under hypoxic conditions in A. thaliana (Chang et al., 2012).

A stable supply of energy is indispensable for plants to withstand various stresses. Under flooding stress conditions, plants experience limited energy supply for their metabolic processes while having restricted soluble sugar content. Therefore, efficient sugar metabolism is crucial for plants to withstand damage caused by flooding stress. In Alfalfa, starch and sucrose metabolism related proteins were largely enriched during waterlogging stress (Zeng et al., 2019). It was reported that sucrose/starch metabolism and glycolysis were inhibited during flooding treatment of soybean seedlings, while plant-derived effectively alleviated the inhibition and enhances soybean growth during recovery from flooding stress. However, growth resumed due to the accumulation of amylase, glucan phosphorylase, and 4-glucan transferase proteins associated with starch and sucrose metabolism (Li et al., 2018b). In cotyledon of soybean, a total of 165 proteins were identified under flooding stress. Among them, 13 proteins were related to sucrose metabolism, indicating the importance of sucrose metabolism during plant responses to flooding stress (Kamal et al., 2015). Furthermore, millimeter wave irradiation on soybean seedlings activated sugar metabolism such as trehalose synthesis and positively regulated soybean growth under waterlogging stress by modulating glycolysis and REDOX-related pathway proteins (Zhong et al., 2020). Furthermore, barley subjected to waterlogging stress exhibited elevated expression levels of pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), GST, as well as other proteins associated with photosynthesis, metabolism, and energy (Luan et al., 2018). Oxidative phosphorylation also occurs under flooding stress conditions. Yan et al. speculated that this ability may primarily originate from aleurone cells, as microscopic observation revealed a high abundance of mitochondria in these cells, which can provide energy for oxidative phosphorylation in the wheat seed endosperm (Yan et al., 2021). The study further demonstrated a significant down-regulation of proteins with peptidase activity or proteasome complexes under flooding stress. All these findings indicate that various plants employ distinct strategies to modulate their sugar metabolism to maintain energy homeostasis and adapt to the challenges posed by waterlogging.

Protein phosphorylation serves as a common post-translational regulatory mechanism enabling plants, such as A. thaliana, wheat, K. candel, and rapeseed, to acquire stable energy supply during flooding stress response (Mao et al., 2010; Chang et al., 2012; Pan et al., 2018; Xu et al., 2018).

The accumulation of proteins associated with cell wall metabolism plays a crucial role in enhancing flooding tolerance in soybeans. Experimental evidence suggests that smoke treatment can enhance soybean growth by increasing the protein abundance and gene expression of O-fucosyltransferase family proteins associated with cell wall remodeling, thereby improving post-flooding survival rates (Li et al., 2018b). Similarly, melatonin supplementation has been shown to enrich proteins involved in cell wall metabolism and enhance plant resilience against flooding stress (Wang et al., 2021b). Under waterlogging conditions, the expression levels of Xyloglucan endotransglycosylase-1 (xet-1) and lignin biosynthesis-related proteins within the cell wall were significantly upregulated in ZS9 (tolerant) and GH01 (sensitive) rapeseed cultivars. This is because plants enhance cell adaptability through cell wall expansion and regulate the synthesis of polysaccharides and lignin to mitigate the impact of abiotic stress, thereby maintaining a balanced biological environment (Xu et al., 2018). Xylan is an indispensable polysaccharide in plant cell wall, and its synthesis is accomplished through xet-1 mediated reaction. In the face of extreme environmental conditions such as flooding, plants up-regulate the expression level of xet-1 gene, thereby promoting the biosynthesis process of xylan to enhance cell wall stability and stress resistance. Polysaccharides and lignin are pivotal constituents of the plant cell wall that not only fortify its stability but also regulate water permeability, preventing excessive expansion caused by over-absorption of water (Liu et al., 2018; Shu et al., 2021). Consequently, under abiotic stress conditions, plants augment polysaccharide and lignin biosynthesis to uphold cell wall integrity and maintain appropriate water permeability.

Moreover, recently developed proteomic techniques, subcellular proteomics, have yielded remarkable findings in elucidating the mechanisms underlying plant responses to flooding (Komatsu et al., 2012; Komatsu and Hashiguchi, 2018). As a powerful tool to elucidate localized cellular responses and subcellular communication, subcellular proteomics has vast potential to understand flooding-response mechanisms in plants. Using this technology, investigators found that flooding exerts a profound impact on the endoplasmic reticulum (ER), as it disrupts protein synthesis and glycosylation processes primarily by altering the protein folding environment and impeding calprotectin/calponin cycle-associated protein folding in soybean roots (Wang and Komatsu, 2016; Komatsu and Hashiguchi, 2018).

Flooding induces hypoxic conditions that impede respiration and metabolism, thereby disrupting the energy supply in plants (Hofmann et al., 2020). However, plants regulate sugar metabolism via the tricarboxylic acid (TCA) cycle and enhance the glycolysis pathway to sustain metabolic energy. In Zostera marina, this strategy is key to growing in the water and adapting to the oxygen-deprived environment. Studies have shown that the expression of glyceraldehyde 3-phosphate and related intermediates in glycolysis pathway is significantly upregulated under anoxic environment in water, thereby promoting anaerobic respiration through glycolysis (Zhang et al., 2021). In Triticum aestivum, both sugar and sugar phosphate are consumed in the germ and roots at temperatures ranging from 24°C to 28°C but not at temperatures between 15°C to 20°C. This indicates that temperature influences both the TCA cycle and sugar metabolism processes, contributing to variations in plant tolerance towards flooding stress (Huang et al., 2018). Flooding treated grape roots convert citric acid into succinic acid and adenosine triphosphate, while exhibiting a significant increase in alanine levels during flooding recovery that remains elevated for one week thereafter (Ruperti et al., 2019). Waterlogging-tolerant rice varieties employ escape strategies to cope with waterlogging stress. A study comparing deep-water variety C9285 with non-deep-water variety Taichung 65 (T65) revealed lower metabolic activity in C9285 under waterlogging conditions. The auxin signaling pathway plays a role in regulating secondary metabolism and carbohydrate metabolism while influencing adventitious root growth. Conjugants IAA-Leu and IAA-Asp exhibit reduced levels in C9285 compared to T65 over time (Fukushima et al., 2020).

Through metabolomic analysis of various plant organs, distinct response and adaptation mechanisms across different organs was observed under flooding events. Taking soybean as an example, under flooding stress, the alanine (Ala), gamma-aminobutyric acid (GABA), sucrose, acetic acid, citric acid, and succinic acid in leaves predominantly decrease; however, these substances show increased accumulation in soybean roots under the same environment (Coutinho et al., 2018). Flooding primarily induces anoxia and osmotic stress in root cells, leading to a reliance on glycolysis and fermentation for ATP production by the roots. Additionally, soybean roots accumulate trehalose (typically present at low levels in plants) to enhance survival under flooding conditions. In contrast to roots experiencing anoxic conditions during flooding stress, leaves do not encounter such oxygen deprivation (Coutinho et al., 2018).

Similarly, in the context of wheat response to flooding, anaerobic root fermentation serves as the primary mechanism for local root adaptation, while carbohydrate metabolism plays a pivotal role in orchestrating the overall systemic response. In addition, the highest content of alanine was found in the metabolite detection of xylem exudates, because alanine not only acts as a nitrogen source supplier, but also as a necessary carrier for carbon skeleton synthesis of glucose to meet the energy demand of wheat in waterlogging (Cid et al., 2023). Similar observations were reported by Jérémy Lothier et al., submerging Medicago truncatula root systems impeded sugar importation resulting in elevated phloem sugar reservoirs and reduced organic acid content; thus negatively regulated sugar metabolism in leaves and other aboveground tissues (Lothier et al., 2020).

Amino acid metabolites, such as asparagine, arginine, and homoserine, decrease over time, whereas osmotic fluid-associated metabolites accumulate, like raffinose, galactinol, phenylpropanoids under flooding stress (Fukushima et al., 2020). Wheat tolerant varieties, like rice, employ escape strategies. Principal component analysis (PCA) of wheat cultivars Frument (intolerant) and Jackson (tolerant) revealed that flooding intolerant wheat varieties exhibited stronger metabolic reactions. Additionally, the results demonstrated that proline accumulation in tolerant varieties was a feedback response to flooding, aiding in the inhibition of lipid peroxidation during inundation. Notably, at the end of the submergence period, intolerant varieties experienced a significant increase in malondialdehyde (MDA) levels, leading to cell membrane damage (Herzog et al., 2018).

Although waterlogging has detrimental effects on plants, they can serve as a source of inspiration. The wild chrysanthemum, “Hangju”, is an authentic medicinal material containing flavonoids as its primary medicinal constituents. It has been observed that flooding-induced stress influences the expression of key enzymes involved in the synthesis pathway of flavonoids, thereby augmenting the accumulation of flavonoids and enhancing the efficacy of “Hangju” to a certain extent (Wang et al., 2019). Similarly, flooding exerts an influence on orchardgrass roots, thereby impacting crucial metabolic pathways such as flavonoid and amino acid metabolism (Shang et al., 2023).