Flooding stress: acclimations and genetic diversity

Advances in plant oxygen sensing: endogenous and exogenous mechanisms

Oxygen is essential for the biochemical processes that sustain life in eukaryotic organisms. Although plants produce oxygen through photosynthesis, they often struggle to survive in low-oxygen environments, such as during flooding or submergence. To endure these conditions, they must reprogram their developmental and metabolic networks, and the adaptation process involves the continuous detection of both exogenous hypoxic signals and endogenous oxygen gradients. Recent research has significantly advanced our understanding of how plants respond to both endogenous and exogenous hypoxia signals. In this review, we explore advancements in both areas, comparing them to responses in animals, with a primary focus on how plants perceive and respond to exogenous hypoxic conditions, particularly those caused by flooding or submergence, as well as the hypoxia signaling pathways in different crops. Additionally, we discuss the interplay between endogenous and exogenous hypoxia signals in plants. Finally, we discuss future research directions aimed at improving crop resilience to flooding by integrating the perception and responses to both endogenous and exogenous signals. Through these efforts, we aspire to contribute to the development of crop varieties that are not only highly resistant but also experience minimal growth and yield penalties, thereby making substantial contributions to agricultural science.

The m6A Reader MhYTP2 Regulates MdERF54 mRNA Stability and Contributes to Hypoxia Tolerance in Apple (Malus domestica)

Hypoxia is one of the main challenges in apple (Malus domestica) cultivation. However, breeding hypoxia-tolerant cultivars demands a thorough understanding of the responses of apple trees to low oxygen supply. Studies have indicated that N6-methyladenosine (m6A) reader regulates plant stress response by binding to their corresponding mRNA targets with m6A modification. The present study investigated the function and mechanism of apple m6A reader MhYTP2 under hypoxia stress. Here, we found that the overexpression of MhYTP2 improved hypoxia resistance in apple. Previous RNA immunoprecipitation sequencing (RIP-seq) results identified the mRNA of Ethylene Response Factor 54 (ERF54) as a direct target of MhYTP2; electronic mobility shift assays (EMSA) further verified this finding. Further transcription inhibition assays demonstrated that MhYTP2 increased MdERF54 mRNA stability. Under hypoxia stress, MdERF54 increased the activities of pyruvate decarboxylase (PDC), lactate dehydrogenase (LDH), and alcohol dehydrogenase (ADH) the key enzymes in anaerobic respiration pathway, activated the ethylene signalling pathway, increased the chlorophyll content of plant leaves and photosynthetic rates, enhanced the adaptability of roots, reduced the damage to biofilm and antioxidant system, and enhanced the antioxidant capacity. Thus, our results elucidated the molecular mechanisms by which the MhYTP2-MdERF54 module influences the response of the apple to hypoxia stress.

Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome

Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.

Transcriptome analysis reveals the role of microbial volatile 3-methyl-1-butanol-induced salt stress tolerance in rice (Oryza sativa L.) seedlings through antioxidant defense system

Microorganisms produce volatile organic compounds (VOCs) that have biological impacts on plants; however, it is unknown how these molecules participate in plants' responses to abiotic stress. This study aimed to determine the potential benefit of 3-methyl-1-butanol (3 MB), a microbial VOC, in helping rice (Oryza sativa) seedlings suffering from salinity stress. Our study revealed that rice seedlings primed with microbial volatile 3 MB for 12 h before exposure to salinity stress could decrease reactive oxygen species (ROS) generation and cell damage in rice roots. Additionally, antioxidant systems such as peroxidase (POD) isozymes 4 and 5 and catalase 1 (CAT1) increased after treatment with 3 MB + NaCl. The microbial volatile 3 MB fumigation also raised the proline content and activated the proline-related genes under 3 MB + NaCl treatment. To further elucidate the molecular mechanisms by which 3 MB assists rice in tolerating salinity stress, transcriptomic analysis was used to investigate the genome-wide gene expressions. Totally, 287 up-regulated differentially expressed genes (DEGs) were found. They are associated with phytohormone regulation, transcription factors, redox signaling, and defense responses. Through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and MapMan enrichment results of DEGs revealed that 3 MB could activate antioxidant systems, jasmonic acid (JA) pathway, and starch biosynthesis to generate more ATP, thus building a line of defense in response to salinity stress. This study provides valuation information indicating that microbial volatile 3 MB vapor can enhance salt stress tolerance in rice seedlings and clarify its underlying mechanism.

Genome-wide identification and expression analysis of the ADH gene family in Artemisia annua L. under UV-B stress

ADHs are key genes that catalyze the interconversion between alcohols and aldehydes, which play crucial roles in plant adaptation to a range of abiotic stresses. However, the characterization and evolutionary pathways of ADH genes in the antimalarial plant Artemisia annua are still unclear. This study identified 49 ADH genes in A. annua and conducted a detailed analysis of their structural features, conserved motifs, and duplication types, revealing that tandem and dispersed duplications are the primary mechanisms of gene expansion. Evolutionary analysis of ADH genes between A. annua (AanADH) and A. argyi (AarADH) revealed dynamic changes, with 35 genes identified deriving from their most recent common ancestor in both species. ADH1, crucial for artemisinin production, had two copies in both species, expanding via dispersed duplication in A. annua but whole-genome duplication in A. argyi. CREs and WGCNA analysis suggested that AanADH genes may be regulated by UV-B stress. Following short-term UV-B treatment, 16 DEGs were identified, including ADH1 (AanADH6 and AanADH7), and these genes were significantly downregulated after two hours treatment (UV2h) and upregulated after four hours treatment (UV4h). The expression changes of these genes were further confirmed by GO enrichment analysis and qRT-PCR experiments. Overall, this study comprehensively characterized the ADH gene family in A. annua and systematically identified AanADH genes that were responsive to UV-B stress, providing a foundation for further research on their roles in abiotic stress responses.

Physiological and Transcriptional Responses of Sesame (Sesamum indicum L.) to Waterlogging Stress

Waterlogging stress significantly impacts the growth and productivity of crops. As a traditional oil crop, sesame (Sesamum indicum L.) suffers substantial damage due to waterlogging stress. However, the mechanism underlying waterlogging stress in sesame is still unclear. In this study, we investigated the physiological indicators of two sesame genotypes under waterlogging stress. The results revealed that the activity of antioxidant enzymes in sesame was affected, with the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2) significantly increased. Additionally, transcriptional analysis identified a total of 15,143 differentially expressed genes (DEGs). Among them, 759 DEGs exhibited consistent differential expression across all time points, representing the core waterlogging-responsive genes. Gene Ontology (GO) enrichment analysis indicated that the DEGs were primarily associated with hypoxia, stimulus response, and oxidoreductase enzyme activities. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were mainly enriched in the metabolic and biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, MAPK signaling pathway-plant, carbon fixation by Calvin cycle, plant hormone signal transduction, and plant-pathogen interaction pathways. Furthermore, transcription factors (TFs) such as AP2/ERF, bHLH, bZIP, and WRKY may play key roles in the transcriptional changes induced by waterlogging stress. Combined with weighted gene co-expression network analysis (WGCNA) analysis and K-means clustering, a total of 5 hub genes and 56 genes were identified, including F-box protein (Sin09950 and Sin12912), bZIP (Sin04465, Sin00091), WRKY (Sin01376, Sin06113), and so on. In brief, this study explored the regulatory network involved in waterlogging stress in sesame at the transcriptome level, providing valuable insights into unraveling the molecular mechanisms of waterlogging stress and facilitating the breeding of improved waterlogging-tolerant sesame varieties.

Survival mechanisms of plants under hypoxic stress: Physiological acclimation and molecular regulation

Hypoxia (low-oxygen tension) caused by complete submergence or waterlogging is an abiotic stress factor that severely affects the yield and distribution of plants. To adapt to and survive under hypoxic conditions, plants employ several physiological and molecular strategies that integrate morphological acclimation, metabolic shifts, and signaling networks. Group VII ETHYLENE RESPONSE FACTORS (ERF-VIIs), master transcription factors, have emerged as a molecular hub for regulating plant hypoxia sensing and signaling. Several mitogen-activated protein kinases and calcium-dependent protein kinases have recently been reported to be involved in potentiating hypoxia signaling via interaction with and phosphorylation of ERF-VIIs. Here, we provide an overview of the current knowledge on the regulatory network of ERF-VIIs and their post-translational regulation in determining plant responses to hypoxia and reoxygenation, with a primary focus on recent advancements in understanding how signaling molecules, including ethylene, long-chain acyl-CoA, phosphatidic acid, and nitric oxide, are involved in the regulation of ERV-VII activities. Furthermore, we propose future directions for investigating the intricate crosstalk between plant growth and hypoxic resilience, which is central to guiding breeding and agricultural management strategies for promoting flooding and submergence stress tolerance in plants.

Molecular mechanisms of nitric oxide regulating high photosynthetic performance of wheat plants in waterlogging at flowering

Nitric oxide (NO) positively contributes to maintaining a high photosynthetic rate in waterlogged-wheat plants by maintaining high stomatal conductance (gs), mesophyll conductance (gm), and electron transport rates in PSII (J). However, the molecular mechanisms underlying the synergistic regulation of photosynthetic characteristics during wheat waterlogging remain unclear. Pot experiments were conducted with two cultivars: Yangmai15 (YM15: high waterlogging-tolerance capacity) and Yangmai24 (YM24: conventional waterlogging-tolerance capacity). The 2 cm waterlogging depth treatment (WL), exogenous spraying of NO every two days in the WL treatment (WLsnp), and suitable soil water content treatment (CK) were established during the flowering stage for eight consecutive days. RNA-seq, weighted gene co-expression network analysis (WGCAN), and protein interaction analysis were performed on the 8th day to screen key genes that maintain high photosynthetic performance in waterlogged-wheat plants. The results indicated that cultivar YM24 and YM15 contained 10411 and 10582 differentially expressed genes (DEGs), respectively. The WL treatment had obviously higher DEGs than the WLsnp treatment compared to the CK treatment. Based on the WGCAN method, the DEGs were clustered into eight modules and correlated significantly with the four photosynthetic parameters mentioned above (P < 0.05). Only the DEGs in the ivory module (571) enriched the photosynthetic pathways among the eight modules. In the ivory module, 10 hub genes, including TaB1274F11.29-1, TaT6H20.190, TaOSNPB_100100300, TaLHCB, TaPSAG, TaCAP10B, TaFAD7A-1, TaCAB3C, TaT27G7, and TaF24G24.140, were screened using the co-expression network method because the genes exhibited similar variation trends with gs, gm, or J across the three water treatments and both cultivars. TaLHCB and TaCAP10B exhibited significant linear relationships with the three parameters of gs, gm, and J (P < 0.05). Consequently, TaLHCB and TaCAP10B genes are defined as waterlogging-resistance genes due to the synergistic regulation of photosynthetic characteristics in waterlogging. Both genes were significantly down-regulated in the WL treatment compared to CK treatment in both cultivars. However, there was no significant difference between WLsnp and CK treatments for the genes in the cultivar YM15. These results suggest that the positive effects of spraying NO with high waterlogging resistance capacities are linked to maintaining high expression levels of key genes and obtaining high photosynthetic characteristics during waterlogging, particularly for cultivars with high waterlogging resistance.

Autophagy Regulates Plant Tolerance to Submergence by Modulating Photosynthesis

The increase in global climate variability has increased the frequency and severity of floods, profoundly affecting agricultural production and food security worldwide. Autophagy is an intracellular catabolic pathway that is dispensable for plant responses to submergence. However, the physiological role of autophagy in plant response to submergence remains unclear. In this study, a multi-omics approach was applied by combining transcriptomics, proteomics, and lipidomics to characterize molecular changes in the Arabidopsis autophagy-defective mutant (atg5-1) responding to submergence. Our results revealed that submergence resulted in remarkable changes in the transcriptome, proteome, and lipidome of Arabidopsis. Under submerged conditions, the levels of chloroplastidic lipids, including monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), and phosphatidylglycerol (PG), were lower in atg5-1 than in wild-type, suggesting that autophagy may affect photosynthesis by regulating lipid metabolism. Consistently, photosynthesis-related proteins and photosynthetic efficiency decreased in atg5-1 under submergence conditions. Phenotypic analysis revealed that inhibition of photosynthesis resulted in a decreased tolerance to submergence. Compared to wild-type plants, atg5-1 plants showed a significant decrease in starch content after submergence. Collectively, our findings reveal a novel role for autophagy in plant response to submergence via the regulation of underwater photosynthesis and starch content.

Differential regulation of the "phytoglobin-nitric oxide respiration" in Medicago truncatula roots and nodules submitted to flooding

Flooding induces hypoxia in plant tissues, impacting various physiological and biochemical processes. This study investigates the adaptive response of the roots and nitrogen-fixing nodules of Medicago truncatula in symbiosis with Sinorhizobium meliloti under short-term hypoxia caused by flooding. Four-week-old plants were subjected to flooding for 1-4 days. Physiological parameters as well as the expression of the senescence marker gene MtCP6 remained unchanged after 4 days of flooding, indicating no senescence onset. Hypoxia was evident from the first day, as indicated by the upregulation of hypoxia marker genes (MtADH, MtPDC, MtAlaAT, MtERF73). Nitrogen-fixing capacity was unaffected after 1 day but markedly decreased after 4 days, while energy state (ATP/ADP ratio) significantly decreased from 1 day and was more affected in nodules than in roots. Nitric oxide (NO) production increased in roots but decreased in nodules after prolonged flooding. Nitrate reductase (NR) activity and expression of genes associated with Phytoglobin-NO (Pgb-NO) respiration (MtNR1, MtNR2, MtPgb1.1) were upregulated, suggesting a role in maintaining energy metabolism under hypoxia, but the use of M. truncatula nr1 and nr2 mutants, impaired in nitrite production, indicated the involvement of these two genes in ATP regeneration during initial flooding response. The addition of sodium nitroprusside or tungstate revealed that Pgb-NO respiration contributes significantly to ATP regeneration in both roots and nodules under flooding. Altogether, these results highlight the importance of NR1 and Pgb1.1 in the hypoxic response of legume root systems and show that nodules are more sensitive than roots to hypoxia.

Harnessing the dynamics of plant organic acids metabolism following abiotic stresses

Plants encounter various environmental stresses throughout development, including shade, high light, drought, hypoxia, extreme temperatures, and metal toxicity, all of which adversely affect growth and productivity. Organic acids (OAs), besides serving as intermediates in the tricarboxylic acid (TCA) cycle, play crucial roles in multiple metabolic pathways and cellular compartments, including mitochondrial metabolism, amino acid metabolism, the glyoxylate cycle, and the photosynthetic mechanisms of C4 and CAM plants. OAs contribute to stress tolerance by acting as root chelating agents, regulating ATP production, and providing reducing power for detoxifying reactive oxygen species (ROS). They also participate in the biosynthesis of solutes involved in stress signaling and osmoregulation, particularly during stomatal movements. This review explores how OAs regulate plant metabolism in response to specific abiotic stresses, emphasizing the increased production of malate, citrate, and succinate, which enhance resilience to water deficits, metal toxicity, and flooding. Since these mechanisms involve intricate metabolic networks, changes in OA metabolism present promising and underexplored potential for agriculture. Understanding these mechanisms could lead to innovative strategies for developing crops with greater resilience to climate change, whether through genetic manipulation or by selecting varieties with favorable metabolic responses to stress.

Response of wheat crop to water-logged conditions under different land configurations and nutrient management

By 2050, the global population is expected to increase from 7.7 billion to 9.7 billion, and wheat will remain crucial for ensuring food security worldwide. It supplies food for more than 4.5 billion individuals in 94 countries and constitutes 40% of the primary diet for the global population. It also has 20% protein and 21% calories. An important concern for wheat cultivation is waterlogging stress, which may escalate in occurrence and intensity due to climate change. The raised bed planting pattern was created to reduce the negative impact of waterlogging stress on wheat productivity. The study was conducted during the rabi seasons of 2017-2018 and 2018-2019 to assess the impact of various nutrient management practices on the growth, yield, and yield characteristics of wheat using flat and raised bed planting methods at the crop research farm in Punjab. The study found that wheat cultivated using a raised bed system with recommended nitrogen, phosphorus, and potassium showed significantly improved plant height (105.28 cm), number of effective tillers per plant (25.08), spike length (11.67 cm), number of grains per spike (72.50), grain yield (6.97 t/ha), and straw yield (9.39 t/ha) compared to traditional planting techniques. Furthermore, these investigations need to be repeated at various locations with various agro-climatic circumstances.

A review of soil waterlogging impacts, mechanisms, and adaptive strategies

Waterlogging is a major abiotic stress affecting plant growth and productivity. Regardless of rainfall or irrigated environments, plants frequently face waterlogging, which may range from short-term to prolonged durations. Excessive precipitation and soil moisture disrupt crop growth, not because of the water itself but due to oxygen deficiency caused by water saturation. This lack of oxygen triggers a cascade of detrimental effects. Once the soil becomes saturated, oxygen depletion leads to anaerobic respiration in plant roots, weakening their respiratory processes. Waterlogging impacts plant morphology, growth, and metabolism, often increasing ethylene production and impairing vital physiological functions. Plants respond to waterlogging stress by altering their morphological structures, energy metabolism, hormone synthesis, and signal transduction pathways. This paper synthesizes findings from previous studies to systematically analyze the effects of waterlogging on plant yield, hormone regulation, signal transduction, and adaptive responses while exploring the mechanisms underlying plant tolerance to waterlogging. For instance, waterlogging reduces crop yield and disrupts key physiological and biochemical processes, such as hormone synthesis and nutrient absorption, leading to deficiencies of essential nutrients like potassium and calcium. Under waterlogged conditions, plants exhibit morphological changes, including the formation of adventitious roots and the development of aeration tissues to enhance oxygen transport. This review also highlighted effective strategies to improve plant tolerance to waterlogging. Examples include strengthening field management practices, applying exogenous hormones such as 6-benzylaminopurine (6-BA) and γ-aminobutyric acid (GABA), overexpressing specific genes (e.g., ZmEREB180, HvERF2.11, and RAP2.6L), and modifying root architecture. Lastly, we discuss future challenges and propose directions for advancing research in this field.

Host plant flooding stress in soybeans differentially impacts avirulent and virulent soybean aphid (Aphis glycines) biotypes

Insect herbivore evolution is tightly linked to changes in their host plants. Many plants have defensive traits that enable them to naturally tolerate and/or deter insect herbivory (host plant resistance; HPR). Some insects have adapted to overcome or resist these defenses (virulence). Global climate change may exacerbate insect virulence, although these interactions have not been closely examined. We tested how one abiotic stressor, flooding, affects interactions between soybeans and two different biotypes of the invasive, soybean aphid (Aphis glycines). In laboratory assays, flooding suppressed avirulent aphid population growth but had no impact on virulent conspecifics, indicating a differential fitness response between biotypes. We also used RNA sequencing to compare flooding stress impacts on gene expression in virulent and avirulent aphids. There were strong, constitutive differences between biotypes regardless of flooding stress, with virulent aphids upregulating putative effector genes and differentially expressing genes involved in epigenetic regulatory processes. Within each biotype, transcriptomic changes due to flooding were limited, but overall, fewer genes were differentially expressed in virulent aphids in response to stress treatments. Our data suggested that virulence adaptations in soybean aphids may also confer greater resiliency to abiotic stress, which could accelerate selection for virulence as climate change effects intensify.

Surviving floods: Escape and quiescence strategies of rice coping with submergence

Historical and recent insights into the molecular mechanisms of escape and quiescence strategies employed by rice to survive flooding.

Comprehensive transcriptome and proteome analysis revealed the molecular mechanisms of melatonin priming and waterlogging response in peach

Waterlogging substantially hampers the growth and development of plants. The escalating trajectory of global climate change is heightening both the frequency and intensity of waterlogging events. Peach trees are particularly vulnerable to waterlogging, with the resultant hypoxia in the rhizosphere profoundly influencing their growth and productivity. This study explored the responses of peach seedlings to waterlogging and the regulatory effects of melatonin priming. After a 24-h waterlogging treatment, a significant increase in relative electrical conductivity and an accumulation of reactive oxygen species were observed, ion permeability was markedly alleviated by melatonin priming. Transcriptomic and proteomic analyses were conducted on peach root samples to elucidate the molecular mechanisms involved in the response to waterlogging and melatonin priming. Transcriptome analysis implicated genes related to 'DNA-binding transcription factor activity', such as AP2/ERF, HSF and WRKY transcription factors, in response to waterlogging. The glycolysis/gluconeogenesis pathway was also significantly enriched, indicating its critical role in the metabolic response to waterlogging. A correlation analysis between differentially expressed genes and proteins highlighted the regulation of numerous genes at both the transcriptional and translational levels. Furthermore, core DEGs/DEPs, including heat shock proteins and stress-related proteins, were identified. Notably, ERF VII member ERF071 (Prupe.8G264900), ADH (Prupe.8G018100), and PCO (Prupe.7G011000) emerged as potential targets for genetic manipulation to enhance waterlogging tolerance in peach. This research provides targets for breeding waterlogging-tolerant varieties and strategies to mitigate waterlogging stress in peach.

Transcriptomic analysis reveals potential roles of polyamine and proline metabolism in waterlogged peach roots inoculated with Funneliformis mosseae and Serendipita indica

Root-associated endophytic fungi can create symbiotic relationships with trees to enhance stress tolerance, but the underlying mechanisms, especially with regard to waterlogging tolerance, remain unclear. This study aimed to elucidate the effects of Funneliformis mosseae and Serendipita indica on the growth, root cross-section structure, and root transcriptional responses of peach under waterlogging stress, with a focus on polyamine and proline metabolism. Genes and transcription factors associated with secondary cell wall biosynthesis were selected, and their expression profiles were analyzed. Funneliformis mosseae significantly increased the height, stem diameter and leaf number of peach seedlings subjected to 2 weeks of waterlogging stress, whereas S. indica only significantly improved stem diameter. Both fungal species substantially increased root diameter, stele diameter, the number of late metaxylem inside the stele and late metaxylem diameter, thus improving aeration within inoculated roots under waterlogging stress. Transcriptomic analysis of waterlogged roots identified 5425 and 5646 differentially expressed genes following inoculation with F. mosseae and S. indica, respectively. The arginine and proline metabolism and arginine biosynthesis pathways were enriched following fungal inoculations. Both fungi reduced the conversion of glutamate and ornithine for proline synthesis. However, S. indica promoted peptide-to-proline conversion by up-regulating the expression of PIPs. Although both fungi promoted the expression of genes involved in arginine and ornithine synthesis pathway, only F. mosseae led to increased levels of arginine and ornithine. Additionally, F. mosseae promoted the accumulation of putrescine and maintained polyamine homeostasis by down-regulating PAO2 and SAMDC. Moreover, F. mosseae facilitated the metabolism of cadaverine. In conclusion, both F. mosseae and S. indica formed symbiotic relationships with peach plants, with F. mosseae primarily improving polyamine accumulation and S. indica predominantly facilitating proline accumulation for enhanced waterlogging resistance.

Could flooding undermine progress in building climate-resilient crops?

Flooding threatens crop productivity, agricultural sustainability, and global food security. In this article I review the effects of flooding on plants and highlight three important gaps in our understanding: (i) effects of flooding on ecological interactions mediated by plants both below (changing root metabolites and exudates) and aboveground (changing plant quality and metabolites, and weakening the plant immune system), (ii) flooding impacts on soil health and microorganisms that underpin plant and ecosystems health, and (iii) the legacy impacts of flooding. Failure to address these overlooked aspects could derail and undermine the monumental progress made in building climate-resilient crops and soil-microbe-assisted plant resilience. Addressing the outlined knowledge gaps will enhance solutions developed to mitigate flooding and preserve gains made to date.

A combination of salt stress and waterlogging provides protection to tomato plants against the negative effects of waterlogging individually applied

Salt stress and waterlogging are two of the most common abiotic stresses in nature, often occurring concurrently. However, our understanding of the mechanisms underlying responses of plants to a combination of these stresses remains limited. In this study, we investigated growth, physiological and biochemical responses of Solanum lycopersicum cv. Micro-Tom to salt stress, waterlogging and the combination of both. Under waterlogging individually, plants showed increased plant height and longer root length. However, they exhibited a significantly smaller leaf area, fewer leaves, reduced fresh and dry weights, and lower relative water content compared to plants grown under controlled conditions. These effects were more severe than those caused by salt stress alone. Interestingly, the growth inhibition from waterlogging was alleviated under combined salt and waterlogging stress. This attenuation may be associated with decreased accumulation of H₂O₂ and oxidized lipids, along with increased proline and photosynthetic pigment contents compared with waterlogging individually applied. However, ROS accumulations and contents of photosynthetic pigments were not straightforwardly linked to the activity of photosynthesis. In addition, activities of various antioxidant enzymes such as CAT, GPX and GST as well as those involved in the AsA-GSH cycle were differently altered by salt stress and waterlogging, individually and in combination. Taken together, these results suggest that the response of tomato plants to salt stress and waterlogging, individually and in combination, can be differently modulated via fine-tuning of acclimation mechanisms to oxidative stress.

A holistic study on the effects of a rural flood detention basin: Flood peaks, water quality and grass growth

Nature-based Solutions (NbS) are widely advocated to have multiple benefits, including in flood risk reduction, water quality improvement and ecosystem health. There are, however, few empirical studies quantifying such multi-functionality. Given the ongoing pressures of flooding and poor water quality within Europe, there is an urgent need for empirical evidence to assess the potential for NbS features to address these issues. We present the first empirical results on the impacts of a nature-based flood detention basin on peak flow attenuation, water quality and pasture health. The detention basin comprised a 1.5m high soil bund constructed within a field bordering a first order tributary on a farm in the south of Ireland. Over two years, peak flows were diverted from the stream channel to the detention basin via a constructed sluice during the rising limb of high discharge. Detained waters were returned slowly to the channel via drainage pipes. During this time hydrological and quality data were collected from upstream, downstream and within the detention basin during peak flow events and pasture sward growth and health within the detention basin was assessed. These data revealed marked peak flow attenuation by < 38%, except under conditions of prolonged rainfall. The detention basin sequestered suspended solids (Removal efficiency RE 5.35%; p < 0.05) and nitrate (RE 13.37%; p < 0.001), but was a source of soluble reactive (RE -95%; p < 0.001) and particulate phosphorus (RE -83%; p < 0.001). There was no statistically significant reduction in pasture biomass, but higher Chlorophyll a/b ratio of inundated plants indicated reduced photosynthetic efficiency (30.85%; p < 0.001). Whilst capable of reducing peak flows, the mixed results on water quality and pasture health show that the operation of NbS features is complex, and that multi-functionality is not an inherent facet of NbS.

Integrating a novel algorithm in assessing the impact of floods on the genetic diversity of a high commercial value fish (Cyprinidae: Spinibarbus sp.) in Lang Son province of Vietnam

Floods, which occur when the amount of precipitation surpasses the capacity of an area to drain it adequately, have detrimental consequences on the survival and future generations of fishes. However, few works have reported the prediction of this natural phenomenon in a relation to certain fish species, especially in fast-flowing rivers. In the specific context of the northern mountainous provinces of Vietnam, where the Spinibarbus sp. fish species resides, it has been observed through the current study that the fish population in Lang Son exhibits the lowest genetic diversity and genetic distance. Consequently, the population of Spinibarbus sp. in Lang Son shows a heightened susceptibility to floods, resulting in reduction in population size and compromised population resilience. In order to provide decision support information for managers, conservationists, and researchers, we have employed a genetic algorithm-support vector machine regression (GA-SVR) predictive model to map flood vulnerability using thirteen dependent variables. The study findings have unveiled a significant negative correlation between flood-sensitive regions and genetic diversity. These discoveries emphasize the significance of considering the impact of floods on the genetic diversity of Spinibarbus sp. in Lang Son through flood vulnerability mapping. This underscores the value of establishing a comprehensive framework based on the GA-SVR algorithm for early flood detection, thereby facilitating the implementation of effective measures to minimize damages and conserve this commercial fish species.

A mechanistic integration of hypoxia signaling with energy, redox, and hormonal cues

Oxygen deficiency (hypoxia) occurs naturally in many developing plant tissues but can become a major threat during acute flooding stress. Consequently, plants as aerobic organisms must rapidly acclimate to hypoxia and the associated energy crisis to ensure cellular and ultimately organismal survival. In plants, oxygen sensing is tightly linked with oxygen-controlled protein stability of group VII ETHYLENE-RESPONSE FACTORs (ERFVII), which, when stabilized under hypoxia, act as key transcriptional regulators of hypoxia-responsive genes (HRGs). Multiple signaling pathways feed into hypoxia signaling to fine-tune cellular decision-making under stress. First, ATP shortage upon hypoxia directly affects the energy status and adjusts anaerobic metabolism. Secondly, altered redox homeostasis leads to reactive oxygen and nitrogen species (ROS and RNS) accumulation, evoking signaling and oxidative stress acclimation. Finally, the phytohormone ethylene promotes hypoxia signaling to improve acute stress acclimation, while hypoxia signaling in turn can alter ethylene, auxin, abscisic acid, salicylic acid, and jasmonate signaling to guide development and stress responses. In this Update, we summarize the current knowledge on how energy, redox, and hormone signaling pathways are induced under hypoxia and subsequently integrated at the molecular level to ensure stress-tailored cellular responses. We show that some HRGs are responsive to changes in redox, energy, and ethylene independently of the oxygen status, and we propose an updated HRG list that is more representative for hypoxia marker gene expression. We discuss the synergistic effects of hypoxia, energy, redox, and hormone signaling and their phenotypic consequences in the context of both environmental and developmental hypoxia.

Shoot hydraulic impairments induced by root waterlogging: Parallels and contrasts with drought

Soil waterlogging and drought correspond to contrasting water extremes resulting in plant dehydration. Dehydration in response to waterlogging occurs due to impairments to root water transport, but no previous study has addressed whether limitations to water transport occur beyond this organ or whether dehydration alone can explain shoot impairments. Using common bean (Phaseolus vulgaris) as a model species, we report that waterlogging also impairs water transport in leaves and stems. During the very first hours of waterlogging, leaves transiently dehydrated to water potentials close to the turgor loss point, possibly driving rapid stomatal closure and partially explaining the decline in leaf hydraulic conductance. The initial decline in leaf hydraulic conductance (occurring within 24 h), however, surpassed the levels predicted to occur based solely on dehydration. Constraints to leaf water transport resulted in a hydraulic disconnection between leaves and stems, furthering leaf dehydration during waterlogging and after soil drainage. As leaves dehydrated later during waterlogging, leaf embolism initiated and extensive embolism levels amplified leaf damage. The hydraulic disconnection between leaves and stems prevented stem water potentials from declining below the threshold for critical embolism levels in response to waterlogging. This allowed plants to survive waterlogging and soil drainage. In summary, leaf and stem dehydration are central in defining plant impairments in response to waterlogging, thus creating similarities between waterlogging and drought. Yet, our findings point to the existence of additional players (likely chemicals) partially controlling the early declines in leaf hydraulic conductance and contributing to leaf damage during waterlogging.

Metabolic strategies in hypoxic plants

Complex multicellular organisms have evolved in an oxygen-enriched atmosphere. Oxygen is therefore essential for all aerobic organisms, including plants, for energy production through cellular respiration. However, plants can experience hypoxia following extreme flooding events and also under aerated conditions in proliferative organs or tissues characterized by high oxygen consumption. When oxygen availability is compromised, plants adopt different strategies to cope with hypoxia and limited aeration. A common feature among different plant species is the activation of an anaerobic fermentative metabolism to provide ATP to maintain cellular homeostasis under hypoxia. Fermentation also requires many sugar substrates, which is not always feasible, and alternative metabolic strategies are thus needed. Recent findings have also shown that the hypoxic metabolism is also active in specific organs or tissues of the plant under aerated conditions. Here, we describe the regulatory mechanisms that control the metabolic strategies of plants and how they enable them to thrive despite challenging conditions. A comprehensive mechanistic understanding of the genetic and physiological components underlying hypoxic metabolism should help to provide opportunities to improve plant resilience under the current climate change scenario.

Response of Arabidopsis thaliana to Flooding with Physical Flow

Flooding causes severe yield losses worldwide, making it urgent to enhance crop tolerance to this stress. Since natural flooding often involves physical flow, we hypothesized that the effects of submergence on plants could change when combined with physical flow. In this study, we analyzed the growth and transcriptome of Arabidopsis thaliana exposed to submergence or flooding with physical flow. Plants exposed to flooding with physical flow had smaller rosette diameters, especially at faster flow rates. Transcriptome analysis revealed that "defense response" transcripts were highly up-regulated in response to flooding with physical flow. In addition, up-regulation of transcripts encoding ROS-producing enzymes, SA synthesis, JA synthesis, and ethylene signaling was more pronounced under flooding with physical flow when compared to submergence. Although H2O2 accumulation changed in response to submergence or flooding with physical flow, it did not lead to lipid peroxidation, suggesting a role for ROS as signaling molecules under these conditions. Multiple regression analysis indicated possible links between rosette diameter under flooding with physical flow and the expression of Rbohs and SA synthesis transcripts. These findings suggest that pathogen defense responses, regulated by SA and ROS signaling, play crucial roles in plant responses to flooding with physical flow.

Alterations in the Rice Coleoptile Metabolome During Elongation Under Submergence Stress

Plants known as obligate aerobes developed different mechanisms to overcome the damage incurred under oxygen limitation. One of the survival strategies to have commonly appeared in hydrophytic plants is the escape strategy, which accelerates plant axial organs' growth in order to escape hypoxic conditions as soon as possible. The present study aimed to distinguish the alterations in coleoptile elongation, viability and metabolic profiles in coleoptiles of slow- and fast-growing rice varieties. All the parameters were tested at 3, 5 and 7 days after sowing, to highlight changes during seedling development in normal and submerged conditions. The obtained results indicated that coleoptile elongation correlated with higher resistance to oxygen deprivation. GS-MS-based metabolic profiling indicated that coleoptiles of the fast-growing cultivar accumulated higher amounts of sugar phosphates, disaccharides, fatty acid derivatives and sterols, which are important for maintaining growth, membrane stability and viability. The slow-growing variety was characterized by a greater abundance of carboxylates, including lactate and phosphoric acid, indicating an energy crisis and cytosol acidification, leading to cell damage and low tolerance. Therefore, a metabolomics approach could be used for phenotyping (chemotyping) in the large-scale screening of newly developed varieties with higher tolerance to oxygen deprivation.

Environmental genome-wide association studies across precipitation regimes reveal that the E3 ubiquitin ligase MBR1 regulates plant adaptation to rainy environments

In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis, understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species. As the frequency and intensity of extreme precipitation events increase, so are the flooding events resulting from soil water saturation. The subsequent onset of hypoxic stress is one of the leading causes of crop damage and yield loss. By combining genomics and remote sensing data, it is now possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia. Here, using an environmental genome-wide association study (eGWAS) of 934 non-redundant georeferenced Arabidopsis ecotypes, we have identified functional variants of the gene MED25 BINDING RING-H2 PROTEIN 1 (MBR1). This gene encodes a ubiquitin-protein ligase that regulates MEDIATOR25 (MED25), part of a multiprotein complex that interacts with transcription factors that act as key drivers of the hypoxic response in Arabidopsis, namely the RELATED TO AP2 proteins RAP2.2 and RAP2.12. Through experimental validation, we show that natural variants of MBR1 have different effects on the stability of MED25 and, in turn, on hypoxia tolerance. This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response. Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets. This thus supports the need for integration of forward and reverse genetics with robust molecular physiology validation of outcomes.

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.

Effects of Complete Submergence on Growth, Survival and Recovery Growth of Alisma orientale (Samuel.) Juz

Intense precipitations caused by global climate change will result in the occurrence of greater frequencies and longer durations of flooding, influencing the survival and yields of wetland plants. Alisma orientale (Samuel.) Juz., an important traditional medicine with edible scape and inflorescence, naturally grows in wetlands and artificially cultivates in paddy fields prone to flood in China. However, we lack understanding of the effect of complete submergence on A. orientale. Here, experiments with four durations of complete submergence including 5 days (ds), 10 ds, 15 ds and 20 ds followed by 20 ds recovery were performed. In the submergence experiments, the number of, length of and biomass of surviving leaves and the total biomass and new blade biomass were measured; in recovery experiments, number and length of surviving leaves were measured. A. orientale grew out longer new leaves during complete submergence, with a dramatic decline in the biomass of both the leaves and tubers as well as the total biomass at the ends of the submergence experiments. The A. orientale plants had a high survival rate after submergence. The duration of submergence did not influence the time for A. orientale needed to start regrowing. At the end of recovery period, the submerged A. orientale plants generated more leaves, had more surviving leaves, had shorter new leaves and a shorter total length of surviving leaves than the control plants. This study highlights that A. orientale plants can resist at least 20 ds of complete submergence caused by flooding and regrow rapidly after submergence and improves our understanding of the flooding tolerance mechanisms of A. orientale plants.

Distinct molecular responses of mangrove plants to hypoxia and reoxygenation stresses contribute to their resilience in coastal wetland environment

Mangroves adapt to periodical submergence and constitute resilient ecosystems in coastal environments. The question is whether they can sustain long submergence stress when sea level rises as a consequence of climate change. To address this, seedlings of two representative mangrove species that acclimate to low to mid tide (Avicennia marina) and mid to high tide (Kandelia obovata) conditions were treated with continual submergence for 7 days as extended hypoxia, or semi-diurnal cyclic submergence and reoxygenation for 7 days. At specific time points, leaves were collected to construct RNA-Sequencing libraries for gene expression analysis. Through the lens of transcriptome, the initial response of A. marina to submergence was mild but more dramatic after prolong immersion. However, the initial response of K. obovata was drastic and reduced in latitude later, suggesting distinct species-specific responses. After adapting to diurnal cycles, both species minimized transcriptome fluctuations similarly. Metabolically, during initial response, sucrose and starch were converted into glucose for fermentation to increase glycolytic flux, coupled with regeneration of NAD+. The energy amelioration was accompanied by longer term phytohormone regulations where ethylene signal transduction pathway was enhanced, but abscisic acid biosynthesis was reduced. Notably, gibberellic acids biosynthesis increased in A. marina but decreased in K. obovata as a unique feature. Genomic level analysis indicated that only about 30 % of the conserved plant submergence responsive genes were expressed during submergence in these mangroves. The function of an ethylene responsive gene was validated in transgenic Arabidopsis. This research elucidates distinct molecular mechanisms and metabolic pathways that empower A. marina and K. obovata to endure prolonged submergence and hypoxia. By highlighting their unique adaptive strategies in response to rising sea levels, these findings enhance our understanding of mangrove resilience and provide insights for the conservation and management of these essential coastal ecosystems in the face of climate change.

Overexpression of Nicotiana tabacum PIP1;3 enhances root aeration and oxygen metabolism in canola (Brassica napus) plants exposed to root hypoxia

High mortality and reduced growth due to root hypoxia are commonly observed in plants impacted by flooding or soil compaction. Since earlier research suggested that Nicotiana tabacum PIP1;3 may facilitate cell-to-cell oxygen transport, we overexpressed NtPIP1;3 in canola (Brassica napus) and studied the effects on growth, physiological parameters, root oxygen concentrations, and energy metabolism in plants subjected to waterlogging. Compared with wild-type plants (WT), the waterlogged plants overexpressing NtPIP1;3 (OE) maintained higher dry biomass, gas exchange, root hydraulic conductivity, root oxygen concentrations, leaf water potentials, root respiration rates, and root ATP concentrations. Metabolic profiling revealed that overexpressing plants responded to root hypoxia by altering the glycolysis, pyruvate metabolism, and TCA cycle in roots. Moreover, the differences in expression patterns of RAP2.12, RAP2.2, PCO1, and PCO2 in WT and OE canola plants exposed to root hypoxia point to increased oxygen supply to OE roots, which was confirmed by direct measurements of root O2 concentrations. Our results demonstrate that the overexpression of NtPIP1;3 affected plant responses to hypoxia by enhancing their aerobic metabolism and strengthened the notion that some of the plant aquaporins may facilitate oxygen transport.

Physiological, molecular, and morphological adjustment to waterlogging stress in ramie and selection of waterlogging-tolerant varieties

Waterlogging stress is a severe abiotic challenge that impedes plant growth and development. Ramie (Boehmeria nivea L.) is a Chinese traditional characteristic economic crop, valued for its fibers and by-products. To investigate the waterlogging tolerance of ramie and provide the scientific basis for selecting waterlogging-tolerant ramie varieties, this study examined the morphological, physiological, biochemical, and molecular responses of 15 ramie germplasms (varieties) under waterlogging stress. The results revealed varied impacts of waterlogging stress across the 15 ramie varieties, characterized by a decrease in SPAD values, net photosynthesis rates, and relative water content of ramie leaves, along with a significant increase in relative conductivity and the activities of antioxidant enzymes such as SOD, POD, CAT, and APX. Additionally, the levels of soluble sugars, soluble proteins, and free proline exhibited varying degrees of increase. Through Principal Component Analysis (PCA), ZZ_2 and ZSZ_1 were identified as relatively tolerant and susceptible varieties. Transcriptome analysis showed that the differential expressed genes between ZZ_2 and ZSZ_1 were significantly enriched in metabolic pathways, ascorbate and aldarate metabolism, and inositol phosphate metabolism, under waterlogging stress. In addition, the expression of hypoxia-responsive genes was higher in ZZ_2 than in ZSZ_1 under waterlogging stress. These differences might account for the varied waterlogging responses between the two varieties. Therefore, this study explored the morpho-physiological responses of ramie under waterlogging stress and identified the molecular mechanisms involved, providing valuable insights for improving ramie varieties and breeding new ones.

Hypoxia stress: plant's sensing, responses, and tolerance mechanisms

Oxygen (O2) is an inhibiting factor for plant growth and development in submerged and flooding environments. Plants experience different O2 concentrations, such as normoxia, hypoxia, and anoxia, which can change over space and time. Plants have evolved various morphological, physiological, and biochemical adaptations to withstand low O2 stress, many of which have been well investigated. This review provides a detailed analysis of how plants respond to hypoxia, a significant stress factor primarily caused by flooding. Hypoxia affects plants at various cellular, developmental, and environmental levels. This review highlights genetic, molecular, and metabolic adaptations crops employ to cope with O2 deficiency. The roles of various transcription factors (TFs) and gene regulation mechanisms in enabling plants to modulate their physiological responses under hypoxic conditions are notable. The review also identifies a significant gap in research on plant responses during reoxygenation, the phase of returning to normal O2 levels, especially under natural lighting conditions. This transition poses ROS generation and photoinhibition challenges, affecting plant recovery post-hypoxia. We discuss various strategies to enhance plant hypoxia tolerance, including traditional breeding, genetic modification, and grafting techniques. It emphasizes integrating these approaches with a comprehensive understanding of hypoxia sensing and response mechanisms. We underscore the complexity of plant adaptations to hypoxia and the need for continued research in this field, especially in the face of global climate change. This is vital for developing sustainable agricultural practices and ensuring future food security.

Genome-wide identification of alcohol dehydrogenase (ADH) gene family in oilseed rape (Brassica napus L.) and BnADH36 functional verification under salt stress

BACKGROUND

Alcohol dehydrogenase (ADH) is an enzyme that binds to zinc, facilitating the interconversion of ethanol and acetaldehyde or other corresponding alcohols/aldehydes in the pathway of ethanol fermentation. It plays a pivotal role in responding to environmental stress. However, the response of the ADH family to abiotic stress remains unknown in rapeseed.

RESULT

In this study, we conducted a comprehensive genome-wide investigation of the ADH family in rapeseed, encompassing analysis of their gene structure, replication patterns, conserved motifs, cis-acting elements, and response to stress. A total of 47 ADH genes were identified within the rapeseed genome. Through phylogenetic analysis, BnADHs were classified into four distinct clades (I, II, IV, V). Prediction of protein domains revealed that all BnADH members possessed a GroES-like (ADH_N) domain and a zinc-bound (ADH_zinc_N) domain. Analysis of promoter sequences demonstrated that BnADHs contained numerous cis-acting elements associated with hormone and stress responses, indicating their widespread involvement in various biological regulatory processes. Expression profiling under different concentrations of salt stress treatments (0%, 0.4%, 0.8%, 1.0% NaCl) further highlighted the significant role played by the BnADH family in abiotic stress response mechanisms. Overexpression of BnADH36 in rapeseed significantly improved the salt tolerance of rapeseed.

CONCLUSION

The features of the BnADH family in rapeseed was comprehensively characterized in this study, which could provide reference to the research of BnADHs in abiotic stress response.

Plant quiescence strategy and seed dormancy under hypoxia

Plant quiescence and seed dormancy can be triggered by reduced oxygen availability. Under water, oxygen depletion caused by flooding can culminate in a quiescent state, which is a plant strategy for energy preservation and survival. In adult plants, a quiescent state can be activated by sugar starvation, leading to metabolic depression. In seeds, secondary dormancy can be activated by reduced oxygen availability, which creates an unfavourable state for germination. The physical dormancy of some seeds and buds includes barriers to external conditions, which indirectly results in hypoxia. The molecular processes that support seed dormancy and plant survival through quiescence under hypoxia include the N-degron pathway, which enables the modulation of ethylene-responsive factors of group VII and downstream targets. This oxygen- and nitric oxide-dependent mechanism interacts with phytohormone-related pathways to control growth.

Functional Identification of miR2119 Targeting ADHs in Modulating Soybean Resistance to Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is a sedentary endoparasite nematode that results in severe economic losses in soybean crops. miRNAs play crucial roles in plant responses to nematode. However, the role of miR2119 responding to SCN stress in soybean. Here, we demonstrated that the transcript levels of polycistronic precursors containing miR2119 and miR398a were significantly reduced in soybean upon nematode infection. Promoter of the miR2119-398a precursor analysis was conducted containing a GUS reporter gene. GUS activity assays demonstrated a decrease in miR2119-398a promoter during SCN infection. Overexpression of polycistronic precursor miR2119-398a (OE-premiR2119-398a) and miR2119 precursor (OE-premiR2119) rendered soybean more susceptible to SCN. Conversely, silencing miR2119 (STTM2119) increased soybean resistance against SCN. Furthermore, RNA-seq analysis revealed that miR2119 is involved in many defense signaling pathways. GUS reporter gene assays demonstrated that miR2119 targets GmADH1.1a and GmADH1.1b. Functional analysis indicated that ADHs act as a major role in responding to H. glycines by modulating reactive oxygen species (ROS) levels. Together, the findings reveal a novel mechanism by which the polycistronic precursor miR2119-398a coordinately regulates in response to H. glycines. Additionally, miR2119 becomes an essential element contributing to H. glycines by modulating ADH activity and ROS homeostasis in soybean.

Combined salt and low nitrate stress conditions lead to morphophysiological changes and tissue-specific transcriptome reprogramming in tomato

Despite intense research towards the understanding of abiotic stress adaptation in tomato, the physiological adjustments and transcriptome modulation induced by combined salt and low nitrate (low N) conditions remain largely unknown. Here, three traditional tomato genotypes were grown under long-term single and combined stresses throughout a complete growth cycle. Physiological, molecular, and growth measurements showed extensive morphophysiological modifications under combined stress compared to the control, and single stress conditions, resulting in the highest penalty in yield and fruit size. The mRNA sequencing performed on both roots and leaves of genotype TRPO0040 indicated that the transcriptomic signature in leaves under combined stress conditions largely overlapped that of the low N treatment, whereas root transcriptomes were highly sensitive to salt stress. Differentially expressed genes were functionally interpreted using GO and KEGG enrichment analysis, which confirmed the stress and the tissue-specific changes. We also disclosed a set of genes underlying the specific response to combined conditions, including ribosome components and nitrate transporters, in leaves, and several genes involved in transport and response to stress in roots. Altogether, our results provide a comprehensive understanding of above- and below-ground physiological and molecular responses of tomato to salt stress and low N treatment, alone or in combination.

Positive contribution of shoot apex to the growth and flooding tolerance of Hemarthria altissima upon complete submergence

Flooding events tend to destroy the original flood-intolerant vegetation in riparian zones, but the flood-tolerant species can confront the stress, and contribute to the riparian ecosystem. Grass species, Hemarthria altissima, are usually dominant in the riparian zones. This species is considered as good forage which is usually grazed by livestock or mowed by local people. Therefore, the apical tissues of the plants are often removed, and the plants have to grow without stem apexes, during their life cycle. In this study, we aimed to examine the differences in growth performance of intact versus apex-cut individuals of H. altissima upon complete submergence. Two groups of H. altissima plants (with and without shoot apexes) were treated with dark non-submergence and dark complete submergence conditions for 200 days. During the experiment, we measured plant growth, biomass changes in plant organs, and the consumption of non-structural carbohydrates (NSC) by different tissues. During submergence, shoot elongation stopped, and around six lateral buds were developed averagely by each plant without apexes. This growth performance finally caused 60% decline of NSC in underground parts. The relatively intensive consumption of carbohydrates in submerged apex-removed plants induced the 21% stem length decreased under water, which indicated the decreasing submergence tolerance of plants with shoot apex removed. Therefore, we suggest that when using H. altissima for restoring degraded riparian ecosystems, the shoot apexes should be protected from grazing by livestock or harvesting by local people in order to maintain the submergence tolerance of H. altissima.

Evaluating waterlogging stress response and recovery in barley (Hordeum vulgare L.): an image-based phenotyping approach

Waterlogging is expected to become a more prominent yield restricting stress for barley as rainfall frequency is increasing in many regions due to climate change. The duration of waterlogging events in the field is highly variable throughout the season, and this variation is also observed in experimental waterlogging studies. Such variety of protocols make intricate physiological responses challenging to assess and quantify. To assess barley waterlogging tolerance in controlled conditions, we present an optimal duration and setup of simulated waterlogging stress using image-based phenotyping. Six protocols durations, 5, 10, and 14 days of stress with and without seven days of recovery, were tested. To quantify the physiological effects of waterlogging on growth and greenness, we used top down and side view RGB (Red-Green-Blue) images. These images were taken daily throughout each of the protocols using the PSI PlantScreen™ imaging platform. Two genotypes of two-row spring barley, grown in glasshouse conditions, were subjected to each of the six protocols, with stress being imposed at the three-leaf stage. Shoot biomass and root imaging data were analysed to determine the optimal stress protocol duration, as well as to quantify the growth and morphometric changes of barley in response to waterlogging stress. Our time-series results show a significant growth reduction and alteration of greenness, allowing us to determine an optimal protocol duration of 14 days of stress and seven days of recovery for controlled conditions. Moreover, to confirm the reproducibility of this protocol, we conducted the same experiment in a different facility equipped with RGB and chlorophyll fluorescence imaging sensors. Our results demonstrate that the selected protocol enables the assessment of genotypic differences, which allow us to further determine tolerance responses in a glasshouse environment. Altogether, this work presents a new and reproducible image-based protocol to assess early stage waterlogging tolerance, empowering a precise quantification of waterlogging stress relevant markers such as greenness, Fv/Fm and growth rates.

Enhancing Coleoptile Length of Rice Seeds under Submergence through NAL11 Knockout

Submergence stress challenges direct seeding in rice cultivation. In this study, we identified a heat shock protein, NAL11, with a DnaJ domain, which can regulate the length of rice coleoptiles under flooded conditions. Through bioinformatics analyses, we identified cis-regulatory elements in its promoter, making it responsive to abiotic stresses, such as hypoxia or anoxia. Expression of NAL11 was higher in the basal regions of shoots and coleoptiles during flooding. NAL11 knockout triggered the rapid accumulation of abscisic acid (ABA) and reduction of Gibberellin (GA), stimulating rice coleoptile elongation and contributes to flooding stress management. In addition, NAL11 mutants were found to be more sensitive to ABA treatments. Such knockout lines exhibited enhanced cell elongation for coleoptile extension. Quantitative RT-PCR analysis revealed that NAL11 mediated the gluconeogenic pathway, essential for the energy needed in cell expansion. Furthermore, NAL11 mutants reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde under submerged stress, attributed to an improved antioxidant enzyme system compared to the wild-type. In conclusion, our findings underscore the pivotal role of NAL11 knockout in enhancing the tolerance of rice to submergence stress by elucidating its mechanisms. This insight offers a new strategy for improving resilience against flooding in rice cultivation.

The calcium-dependent protein kinase CPK16 regulates hypoxia-induced ROS production by phosphorylating the NADPH oxidase RBOHD in Arabidopsis

Reactive oxygen species (ROS) production is a key event in modulating plant responses to hypoxia and post-hypoxia reoxygenation. However, the molecular mechanism by which hypoxia-associated ROS homeostasis is controlled remains largely unknown. Here, we showed that the calcium-dependent protein kinase CPK16 regulates plant hypoxia tolerance by phosphorylating the plasma membrane-anchored NADPH oxidase respiratory burst oxidase homolog D (RBOHD) to regulate ROS production in Arabidopsis (Arabidopsis thaliana). In response to hypoxia or reoxygenation, CPK16 was activated through phosphorylation of its Ser274 residue. The cpk16 knockout mutant displayed enhanced hypoxia tolerance, whereas CPK16-overexpressing (CPK16-OE) lines showed increased sensitivity to hypoxic stress. In agreement with these observations, hypoxia and reoxygenation both induced ROS accumulation in the rosettes of CPK16-OEs more strongly than in the rosettes of the cpk16-1 mutant or the wild type. Moreover, CPK16 interacted with and phosphorylated the N-terminus of RBOHD at 4 serine residues (Ser133, Ser148, Ser163, and Ser347) that were necessary for hypoxia- and reoxygenation-induced ROS accumulation. Furthermore, the hypoxia-tolerant phenotype of cpk16-1 was fully abolished in the cpk16 rbohd double mutant. Thus, we have uncovered a regulatory mechanism by which the CPK16-RBOHD module shapes the ROS production during hypoxia and reoxygenation in Arabidopsis.

Conversion of lipids into carbohydrates rescues energy insufficiency in rapeseed germination under waterlogging stress

Waterlogging stress, particularly during seed germination, significantly affects plant growth and development. However, the physiological and molecular mechanisms underlying waterlogging stress responses during rapeseed germination remain unclear. In this study, two rapeseed cultivars, Xiangzayou518 (waterlogging-sensitive) and Dadi199 (waterlogging-tolerant), were used to explore the physiological mechanisms underlying rapeseed response to waterlogging stress during germination. Our results showed that waterlogging significantly decreased the emergence percentage and seedling growth rate. During the radicle elongation period (from 48 to 96 h post-germination), the most sensitive period to waterlogging during germination, sugar content, and glycolysis efficiency were significantly decreased, but anaerobic fermentation was enhanced. In tolerant cultivars, when the energy supply was insufficient, the conversion efficiency of lipids into sugar increased, and the activities of isocitrate lyase, malate synthase, and fructose-1, 6-diphosphatase were enhanced by 11.63, 19.06, and 20.37%, respectively, at 72 h post-germination under waterlogging stress. Transcriptome data showed that the differentially expressed genes were significantly enriched in glucose and lipid metabolism pathways when comparing waterlogged stress and normal conditions. These results indicate that waterlogging affects seed germination in rapeseed by inhibiting carbohydrate metabolism, and the conversion capacity of lipids into sugar under waterlogging stress was stronger in tolerant cultivars than in sensitive cultivars, thus rescuing the insufficient energy supply in seed germination and seedling growth. This study reveals the physiological mechanism of rapeseed response to waterlogging stress during seed germination and provides a valuable reference for improving waterlogging tolerance.

Nitric oxide, energy, and redox-dependent responses to hypoxia

Hypoxia occurs when oxygen levels fall below the levels required for mitochondria to support respiration. Regulated hypoxia is associated with quiescence, particularly in storage organs (seeds) and stem cell niches. In contrast, environmentally induced hypoxia poses significant challenges for metabolically active cells that are adapted to aerobic respiration. The perception of oxygen availability through cysteine oxidases, which function as oxygen-sensing enzymes in plants that control the N-degron pathway, and the regulation of hypoxia-responsive genes and processes is essential to survival. Functioning together with reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2) and reactive nitrogen species (RNS), such as nitric oxide (·NO), nitrogen dioxide (·NO2), S-nitrosothiols (SNOs), and peroxynitrite (ONOO-), hypoxia signaling pathways trigger anatomical adaptations such as formation of aerenchyma, mobilization of sugar reserves for anaerobic germination, formation of aerial adventitious roots, and the hyponastic response. NO and H2O2 participate in local and systemic signaling pathways that facilitate acclimation to changing energetic requirements, controlling glycolytic fermentation, the γ-aminobutyric acid (GABA) shunt, and amino acid synthesis. NO enhances antioxidant capacity and contributes to the recycling of redox equivalents in energy metabolism through the phytoglobin (Pgb)-NO cycle. Here, we summarize current knowledge of the central role of NO and redox regulation in adaptive responses that prevent hypoxia-induced death in challenging conditions such as flooding.

New Insights into the Connections between Flooding/Hypoxia Response and Plant Defenses against Pathogens

The impact of global climate change has highlighted the need for a better understanding of how plants respond to multiple simultaneous or sequential stresses, not only to gain fundamental knowledge of how plants integrate signals and mount a coordinated response to stresses but also for applications to improve crop resilience to environmental stresses. In recent years, there has been a stronger emphasis on understanding how plants integrate stresses and the molecular mechanisms underlying the crosstalk between the signaling pathways and transcriptional programs that underpin plant responses to multiple stresses. The combination of flooding (or resulting hypoxic stress) with pathogen infection is particularly relevant due to the frequent co-occurrence of both stresses in nature. This review focuses on (i) experimental approaches and challenges associated with the study of combined and sequential flooding/hypoxia and pathogen infection, (ii) how flooding (or resulting hypoxic stress) influences plant immunity and defense responses to pathogens, and (iii) how flooding contributes to shaping the soil microbiome and is linked to plants' ability to fight pathogen infection.

A UPLC-MS/MS method for quantification of metabolites in the ethylene biosynthesis pathway and its biological validation in Arabidopsis

The plant hormone ethylene is of vital importance in the regulation of plant development and stress responses. Recent studies revealed that 1-aminocyclopropane-1-carboxylic acid (ACC) plays a role beyond its function as an ethylene precursor. However, the absence of reliable methods to quantify ACC and its conjugates malonyl-ACC (MACC), glutamyl-ACC (GACC), and jasmonyl-ACC (JA-ACC) hinders related research. Combining synthetic and analytical chemistry, we present the first, validated methodology to rapidly extract and quantify ACC and its conjugates using ultra-high-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS). Its relevance was confirmed by application to Arabidopsis mutants with altered ACC metabolism and wild-type plants under stress. Pharmacological and genetic suppression of ACC synthesis resulted in decreased ACC and MACC content, whereas induction led to elevated levels. Salt, wounding, and submergence stress enhanced ACC and MACC production. GACC and JA-ACC were undetectable in vivo; however, GACC was identified in vitro, underscoring the broad applicability of the method. This method provides an efficient tool to study individual functions of ACC and its conjugates, paving the road toward exploration of novel avenues in ACC and ethylene metabolism, and revisiting ethylene literature in view of the recent discovery of an ethylene-independent role of ACC.

Arbuscular Mycorrhizal Fungi Mediate the Acclimation of Rice to Submergence

Flooding is a critical factor that limits the establishment of a symbiosis between rice and arbuscular mycorrhizal fungi (AMF) in wetland ecosystems. The distribution of carbon resources in roots and the acclimation strategies of rice to flooding stress in the presence of AMF are poorly understood. We conducted a root box experiment, employing nylon sheets or nylon meshes to create separate fungal chambers that either prevented or allowed the roots and any molecules to pass through. We found that the mycorrhizal colonization rate and the expression of genes OsD14L and OsCERK1, which are involved in fungal perception during symbiosis, both increased in mycorrhizal rice roots following intermittent flooding compared to continuous flooding. Furthermore, AMF inoculation affected root morphological traits, facilitating both shallower and deeper soil exploration. Increased submergence intensity led to carbohydrate deprivation in roots, while high mycorrhizal colonization increased soil oxygen consumption and decreased the neutral lipid concentration in roots. However, mycorrhizal inoculation increased the rice photosynthesis rate and facilitated acclimation to submergence by mediating the expression of the genes OsCIPK15 and OsSUB1A to enhance rice shoot elongation and the sugar concentration in roots as a result of reduced competition for carbon between rice and AMF under different flooding conditions.

N-terminal cysteine acetylation and oxidation patterns may define protein stability

Oxygen homeostasis is maintained in plants and animals by O2-sensing enzymes initiating adaptive responses to low O2 (hypoxia). Recently, the O2-sensitive enzyme ADO was shown to initiate degradation of target proteins RGS4/5 and IL32 via the Cysteine/Arginine N-degron pathway. ADO functions by catalysing oxidation of N-terminal cysteine residues, but despite multiple proteins in the human proteome having an N-terminal cysteine, other endogenous ADO substrates have not yet been identified. This could be because alternative modifications of N-terminal cysteine residues, including acetylation, prevent ADO-catalysed oxidation. Here we investigate the relationship between ADO-catalysed oxidation and NatA-catalysed acetylation of a broad range of protein sequences with N-terminal cysteines. We present evidence that human NatA catalyses N-terminal cysteine acetylation in vitro and in vivo. We then show that sequences downstream of the N-terminal cysteine dictate whether this residue is oxidised or acetylated, with ADO preferring basic and aromatic amino acids and NatA preferring acidic or polar residues. In vitro, the two modifications appear to be mutually exclusive, suggesting that distinct pools of N-terminal cysteine proteins may be acetylated or oxidised. These results reveal the sequence determinants that contribute to N-terminal cysteine protein modifications, with implications for O2-dependent protein stability and the hypoxic response.

Different Phenotypic, Photosynthetic, and Physiological Responses to Flooding between Q. nuttallii and Q. palustris

Flooding stress is an increasingly serious problem in wetlands, often affecting large areas of crops and timber production areas. The current study aimed to explore the species differences in responses to flooding stress between Q. nuttallii and Q. palustris in an outdoor environment. All the tested plants survived after a 60-day flooding treatment that left 5 cm of water above the soil surface. This suggests that the two species are flood-tolerant, so they can be applied in the construction of riparian protection forests and wetland restoration. Compared with control conditions, flooding treatment significantly decreased seedling height and diameter and the Pn, Gs, Tr, Fv/Fm, ABS/CSm, TR0/CSm, ET0/CSm, RE0/CSm, IAA, and GA3 content and significantly increased the content of MDA, H2O2, soluble sugars, SOD, POD, ADH, ABA, and JA. Under control conditions, Q. nuttallii showed significantly greater growth and photosynthetic capability than Q. palustris. In contrast, Q. palustris exhibited less inhibition of growth and photosynthesis, oxidative stress levels, and antioxidant enzyme activities than Q. nuttallii under flooding conditions. The findings indicate that Q. palustris has better defense mechanisms against the damage caused by flooding stress than Q. nuttallii. Q. nuttallii was more sensitive and responsive to flooding than Q. palustris.

Stem elongation and gibberellin response to submergence depth in clonal plant Alternanthera philoxeroides

Clonal plants are widely distributed in the riparian zone and play a very important role in the maintenance of wetland ecosystem function. Flooding is an environmental stress for plants in the riparian zone, and the response of plants varies according to the depth and duration of flooding. However, there is a lack of research on the growth response of clonal plants during flooding, and the endogenous hormone response mechanism of clonal plants is still unclear. In the present study, Alternanthera philoxeroides, a clonal plant in the riparian zone, was used to investigate the time-dependent stem elongation, the elongation of different part of the immature internodes, and the relationship between growth elongation and the phytohormone gibberellin (GA) under a series of submergence depths (0 m, 2 m, 5 m, and 9 m). The results showed that stem elongation occurred under all treatments, however, compared to 0 m (control), plants grew more under 2 m and 5 m submergence depth, while grew less under 9 m water depth. Additionally, basal part elongation of the immature internode was the predominant factor contributing to the stem growth of A. philoxeroides under different submergence depths. The phytohormone contents in basal part of the mature and immature internodes showed that GA induced the differential elongation of internode. Plant submerged at depth of 2 m had the highest GA accumulation, but plant submerged at depth of 9 m had the lowest GA concentration. These data suggested that GA biosynthesis are essential for stem elongation in A. philoxeroides, and the basal part of the immature internode was the main position of the GA biosynthesis. This study provided new information about the rapid growth and invasion of the clonal plant A. philoxeroides around the world, further clarified the effects of submergence depth and duration on the elongation of the stem, and deepened our understanding of the growth response of terrestrial plants in deeply flooded environments.

Individual architecture and photosynthetic performance of the submerged form of Drosera intermedia Hayne

Drosera intermedia grows in acidic bogs in parts of valleys that are flooded in winter, and that often dry out in summer. It is also described as the sundew of the most heavily hydrated habitats in peatlands, and it is often found in water and even underwater. This sundew is the only one that can tolerate long periods of submersion, and more importantly produces a typical submerged form that can live in such conditions for many years. Submerged habitats are occupied by D. intermedia relatively frequently. The aim of the study was to determine the environmental conditions and architecture of individuals in the submerged form of D. intermedia. The features of the morphological and anatomical structure and chlorophyll a fluorescence of this form that were measured were compared with analogous ones in individuals that occurred in emerged and peatland habitats. The submerged form occurred to a depth of 20 cm. Compared to the other forms, its habitat had the highest pH (4.71-4.92; Me = 4.71), the highest temperature and substrate hydration, and above all, the lowest photosynthetically active radiation (PAR; 20.4-59.4%). This form differed from the other forms in almost all of the features of the plant's architecture. It is particularly noteworthy that it had the largest main axis height among all of the forms, which exceeded 18 cm. The number of living leaves in a rosette was notable (18.1 ± 8.1), while the number of dead leaves was very low (6.9 ± 3.8). The most significant differences were in the shape of its submerged leaves, in which the length of the leaf blade was the lowest of all of the forms (0.493 ± 0.15 mm; p < 0.001) and usually the widest. The stem cross-sectional area was noticeably smaller in the submerged form than in the other forms, the xylem was less developed and collaterally closed vascular bundles occurred. Our analysis of the parameters of chlorophyll fluorescence in vivo revealed that the maximum quantum yield of the primary photochemistry of photosystem II is the highest for the submerged form (Me = 0.681), the same as the maximum quantum yield of the electron transport (Me φE0 = 0.183). The efficiency of energy use per one active reaction center of photosystem II (RC) was the lowest in the submerged form (Me = 2.978), same as the fraction of energy trapped by one active RC (Me = 1.976) and the non-photochemical energy dissipation (DI0/RC; Me = 0.916). The ET0/RC parameter, associated with the efficiency of the energy utilization for electron transport by one RC, in the submerged plant reached the highest value (Me = 0.489). The submerged form of D. intermedia clearly differed from the emerged and peatland forms in its plant architecture. The submerged plants had a thinner leaf blade and less developed xylem than the other forms, however, their stems were much longer. The relatively high photosynthetic efficiency of the submerged forms suggests that most of the trapped energy is utilized to drive photosynthesis with a minimum energy loss, which may be a mechanism to compensate for the relatively small size of the leaf blade.