Waterlogging-induced increase in sugar mobilization, fermentation, and related gene expression in the roots of mung bean (Vigna radiata)

Characterization and transformation of the CabHLH18 gene from hot pepper to enhance waterlogging tolerance

Basic helix-loop-helix (bHLH) proteins are important in abiotic stress control. Here, a specific bHLH transcription factor gene, CabHLH18, from a strong waterlogging-tolerant pepper cultivar, 'ZHC2', was successfully cloned. The CabHLH18 gene presented a coding sequence length of 1,056 bp, encoding 352 amino acids, and the protein was the closest to Capsicum annuum XM016694561.2 protein. The CabHLH18 protein was located in the nucleus. The transformation of the CabHLH18 overexpression vector into the plumules of hot peppers, 'DFZJ' and 'ZHC1', exhibited 21.37% and 22.20% efficiency, respectively. The root length, plant height, and fresh weight of the 'DFZJ' overexpression lines were greater than those of wild-type (WT) plants under waterlogging conditions. Compared with the WT plants, the overexpression lines generally showed greater contents of water, the amino acid, proline, soluble sugar, root viability, and superoxide dismutase activity, but lower malondialdehyde content under waterlogging conditions. Plant fresh weight, amino acids, proline, and soluble sugar levels of the overexpression lines were 39.17%, 45.03%, 60.67%, and 120.18% greater, respectively, compared with the WT plants at 24 h after waterlogging stress. Therefore, the CabHLH18 gene could be implicated in conferring waterlogging tolerance in hot peppers and holds promise for enhancing their overall waterlogging tolerance.

Comprehensive evaluation of morphological and physiological responses of seventeen Crassulaceae species to waterlogging and drainage under temperate monsoon climate

Unpredictable rainfall frequently results in excess moisture, which is detrimental to the landscape because it interferes with the genetic, morphological, and physiological processes of plants, even though the majority of urban landscapes frequently experience moisture shortages. A study was conducted to analyze the effects of a 36-day waterlogging phase and a subsequent 12-day recovery period on the morpho-physiological responses of 17 Crassulaceae species with the goal of identifying those which were more tolerant of the conditions. Results revealed that waterlogging stress has an impact on all morpho-physiological parameters. Sensitive materials (S7, Hylotelephium telephium 'Purple Emperor' and S15, S. sexangulare) showed severe ornamental quality damage, mortality, decreases in total dry biomass, root-shoot ratio, and chlorophyll content, as well as higher MDA concentrations. Lower reductions in these parameters, along with improved antioxidant enzyme activities and greater recovery capabilities after drainage, were observed in the most tolerant materials S2 (H. spectabile 'Brilliant'), S3 (H. spectabile 'Carl'), and S5 (H. telephium 'Autumn Joy'). Furthermore, with the exception of early death materials (S7 and S15), all materials showed varying intensities of adventitious root formation in response to waterlogging. The 17 species were divided into 4 clusters based on the comprehensive evaluation value. The first group included S1-S3, S5-S6, S8-S12, which were waterlogged tolerant with the highest values (0.63-0.82). S14 belongs to the intermediate waterlogging tolerant. S4, S13, S16, and S17 were clustered into the low waterlogging-tolerant group. S7 and S15 were the most susceptible to waterlogging. The survival and success of Crassulaceae species (especially, the first and second cluster), throughout this prolonged period of waterlogging (36 days) and recovery were attributed to a combination of physiological and morphological responses, indicating that they are an appealing species for the creation of rain gardens or obstructed drainage locations.

Lead Toxicity-Mediated Growth and Metabolic Alterations at Early Seedling Stages of Maize (Zea mays L.)

To investigate the toxic effects of lead (Pb) on key metabolic activities essential for proper germination and seedling growth of maize seeds, experiments were carried out with different levels of Pb (0 to 120 mg of Pb L-1 as PbCl2) applied through growth medium to two maize hybrids H-3310S and H-6724. The research findings indicated that growth and metabolic activities were adversely affected by increased Pb contamination in growth medium; however, a slow increase in these parameters was recorded with increasing time from 0 to 120 h. Protease activity decreased with an increase in the level of Pb contamination but increased with time; consequently, a reduction in seed proteins and an increase in total free amino acids were observed with time. Similarly, α-amylase activity decreased with an increase in Pb concentration in growth medium while it increased with increasing time from 0 to 120 h; consequently, reducing and non-reducing sugars increased with time but decreased with exposure to lead. The roots of both maize hybrids had higher Pb contents than those of the shoot, which decreased the uptake of nitrogen, phosphorus, and potassium. All these nutrients are essential for optimal plant growth; therefore, the reduction in growth and biomass of maize seedlings could be due to Pb toxicity that altered metabolic processes, as sugar and amino acids are necessary for the synthesis of metabolic compounds, rapid cell division, and proper functioning of enzymes in the growing embryo, but all were dramatically reduced due to suppression of protease and α-amylase by toxicity of Pb. In general, hybrid H-3310S performed better in Pb-contaminated growth medium than H-6724.

Physiological and sucrose metabolic responses to waterlogging stress in balloon flower (Platycodon grandiflorus (Jacq.) A. DC)

Waterlogging stress is a major limiting factor resulting in stunted growth and loss of crop productivity, especially for root crops. However, physiological responses to waterlogging have been studied in only a few plant models. To gain insight into how balloon flower (Platycodon grandiflorus (Jacq.) A. DC) responds to waterlogging stress, we investigate changes to sucrose metabolism combined with a physiological analysis. Although waterlogging stress decreased the photosynthetic rate in balloon flower, leaves exhibited an increase in glucose (ninefold), fructose (4.7-fold), and sucrose (2.1-fold), indicating inhibition of sugar transport via the phloem. In addition, roots showed a typical response to hypoxia, such as the accumulation of proline (4.5-fold higher than in control roots) and soluble sugars (2.1-fold higher than in control roots). The activities and expression patterns of sucrose catabolizing enzymes suggest that waterlogging stress leads to a shift in the pathway of sucrose degradation from invertase to sucrose synthase (Susy), which consumes less ATP. Furthermore, we suggest that the waterlogging-stress-induced gene PlgSusy1 encodes the functional Susy enzyme, which may contribute to improving tolerance in balloon flower to waterlogging. As a first step toward understanding the waterlogging-induced regulatory mechanisms in balloon flower, we provide a solid foundation for further understanding waterlogging-induced alterations in source-sink relationships.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01310-y.

Effects of soil waterlogging and high-temperature stress on photosynthesis and photosystem II of ginger (Zingiber officinale)

Heavy waterlogging and high temperatures occur frequently in North China, yet the effects of changing environments on photochemical reactions and carbon metabolism have not been described in ginger. To determine the impact of waterlogging and high temperature on ginger, in this study, treatment groups were established as follows: (a) well-watered at ambient temperature (28 °C/22 °C) (CK), (b) well-watered at moderate temperature (33 °C/27 °C) (MT), (c) well-watered at high temperature (38 °C/32 °C) (HT), (d) waterlogging at ambient temperature (CK-WL), (e) waterlogging at moderate temperature (MT-WL), and (f) waterlogging at high temperature (HT-WL) during the rhizome growth period. We analyzed the effect of different treatments on the photosynthetic performance of ginger. Here, our results showed that waterlogging and high temperature irreversibly decreased the photosynthetic pigment content, increased the ROS content of leaves, inhibited leaf carbon assimilation and limited PSII electron transport efficiency. In addition, waterlogging in isolation and high temperature in isolation affected photosynthesis to varying degrees. Taken together, photosynthesis was more sensitive to the combined stress than to the single stresses. The results of this research provide deep insights into the response mechanisms of crop photosynthesis to different water and temperature conditions and aid the development of scientific methods for mitigating plant damage over time.

Waterlogging during the reproductive growth stage causes physiological and biochemical modifications in the leaves of cowpea (Vigna unguiculata L.) genotypes with contrasting tolerance

Waterlogging causes various metabolic, physiological, and morphological changes in crops, resulting in yield loss of most legumes in rainfed and irrigated agriculture. However, research on cowpea genotypes using physiological and biochemical traits as a measure of tolerance to waterlogging stress is limited. We evaluated the impacts of 7 days of waterlogging (DOW) and 7 days of recovery (DOR) on the physiology and biochemistry of two cowpea (Vigna unguiculata (L.) Walp) genotypes (UCR 369 and EpicSelect.4) with contrasting waterlogging tolerance. Cowpea genotypes were grown in a controlled environment until the R2 stage and then subjected to 7 DOW. Later, the waterlogged plants were reoxygenated for an additional 7 DOR. Overall, cowpea genotypes had a contrasting response to waterlogging using different mechanisms. Compared to the control, the photosynthetic parameters of both cowpea genotypes were impaired under 7 DOW and could not recover at 7 DOR, with a larger decline in EpicSelect.4.7 DOW caused significant loss in the chlorophyll and carotenoid content of both genotypes. However, only waterlogged UCR 369 was not photo-inhibited and able to restore the levels of chlorophyll and carotenoids at 7 DOR. In addition, 7 DOW induced intense stress in UCR 369 with increased zeaxanthin, sucrose, and flavonoid content, while these metabolites were decreased in EpicSelect.4. On the other hand, glucose, fructose, and phenolic content were increased in EpicSelect.4 but decreased in UCR 369 at 7 DOR. In summary, compared to EpicSelect.4, UCR 369 restored their photosynthetic pigments and metabolites to the control levels at 7 DOR, indicating a likely tolerance to waterlogging stress.

Waterlogging priming alleviates the oxidative damage, carbohydrate consumption, and yield loss in soybean (Glycine max) plants exposed to waterlogging

In this study, we tested whether waterlogging priming at the vegetative stage would mitigate a subsequent waterlogging event at the reproductive stage in soybean [Glycine max (L.) Merr.]. Plants (V3 stage) were subjected to priming for 7days and then exposed to waterlogging stress for 5days (R2 stage) with non-primed plants. Roots and leaves were sampled on the fifth day of waterlogging and the second and fifth days of reoxygenation. Overall, priming decreased the H2 O2 concentration and lipid peroxidation in roots and leaves during waterlogging and reoxygenation. Priming also decreased the activity of antioxidative enzymes in roots and leaves and increased the foliar concentration of phenols and photosynthetic pigments. Additionally, priming decreased fermentation and alanine aminotransferase activity during waterlogging and reoxygenation. Finally, priming increased the concentration of amino acids, sucrose, and total soluble sugars in roots and leaves during waterlogging and reoxygenation. Thus, primed plants were higher and more productive than non-primed plants. Our study shows that priming alleviates oxidative stress, fermentation, and carbohydrate consumption in parallel to increase the yield of soybean plants exposed to waterlogging and reoxygenation.

UHPLC-MS/MS and QRT-PCR profiling of PGP agents and Rhizobium spp. of induced phytohormones for growth promotion in mungbean (var. Co4

In present study, five potential strains with different plant growth promotion (PGP) characteristics were used. By considering various PGP properties of different bacterial strains, several treatments based on various combinations were developed and studied on mungbean (var. Co4). The quantification of the phytohormones was performed on ultrahigh-performance liquid chromatograph coupled to heated electrospray ionization tandem mass spectrometry (UHPLC/HESI-MS/MS). Indole 3-acetic acid (IAA) and Indole 3-butyric acid (IBA) were quantified in positive ionization mode while Gibberellic acid (GA₃) and salicylic acid (SA) were quantified in negative ionization mode. Among all the treatments two penta combinations of consortia 1 (Rhizobium + Azospirillum + Pseudomonas + Bacillus spp. + Bacillus licheniformis) and consortia 2 (Rhizobium + Azotobacter + Pseudomonas + Bacillus spp. + Bacillus licheniformis) were found most effective. Higher amount of IAA (1.043 μg g⁻¹), IBA (0.036 μg g⁻¹), GA₃ (1.999 μg g⁻¹) and SA (0.098 μg g⁻¹) Fresh weight (FW) were found in treated adolescent root tissues of consortia 2 as compared to consortia 1. Moreover, transcriptional level of the plant hormones were 2–4 fold higher in the relative gene expression study of three genes: ARF (Auxin responsive factors), ERF-IF (Ethylene-responsive Initiation Factors) and GAI (Gibberellic-Acid Insensitive) in consortia 2, on the 15^th, 30^th and 45^th day using quantitative real time-Polymerase chain reaction (qRT-PCR). Furthermore, Yield attributing characters like, the number of nodules plant⁻¹, number of pods plant⁻¹, weight of nodule and seed yield plant⁻¹ were also increased as compared to the control. As a result, the current research elucidated that penta combinations consortium of Rhizobium sp. and rhizobacteria can be developed as a single delivery system biofertilizer for enhancing mungbean productivity.

Iron toxicity increases oxidative stress and impairs mineral accumulation and leaf gas exchange in soybean plants during hypoxia

Iron toxicity is a major challenge faced by plants in hypoxic soils; however, the consequences of such combined stress for soybean (Glycine max) remain to be determined. Here we assessed the physiological responses of soybean plants exposed to hypoxia and a high concentration of iron. Soil-grown plants cultivated in a greenhouse until the vegetative stage were transferred to a hydroponic system containing nutrient solution and subjected to two oxygen conditions (normoxia (6.2 mg L-1) and hypoxia (0.33 mg L-1)) and two iron concentrations (Fe-EDTA) (0.09 and 1.8 mM) for 72 h. During hypoxia, high concentrations of iron in the nutrient solution resulted in increased iron accumulation in roots and leaves. Under this condition, the concentrations of zinc, nitrogen, potassium, and calcium decreased in the roots, while the concentration of nitrogen and magnesium decreased in the leaves. Additionally, during hypoxia, the higher concentration of iron led to an increase in the activity of the antioxidant enzymes in roots and leaves, while decreased the levels of the photosynthetic pigments, leaf gas exchange, and plant growth. In conclusion, high iron concentration in the root medium results in a considerably more severe damage condition to soybean plants under hypoxia compared to plants grown under low iron availability.

Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves

Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.

Comparative Proteomic Analysis of Grapevine Rootstock in Response to Waterlogging Stress

Waterlogging severely affects global agricultural production. Clarifying the regulatory mechanism of grapevine in response to waterlogging stress will help to improve the waterlogging tolerance of grapevine. In the present study, the physiological and proteomic responses of SO4 grapevine rootstock to different waterlogging tolerances were comparatively assayed. The results showed that the activities of SOD and POD first increased and then decreased, while the change trend of CAT and APX activities was the opposite. In addition, the MDA and H₂O₂ contents increased after waterlogging treatment, but the chlorophyll a and chlorophyll b contents decreased. A total of 5,578 grapevine proteins were identified by the use of the tandem mass tag (TMT) labeling technique. Among them, 214 (103 and 111 whose expression was upregulated and downregulated, respectively), 314 (129 and 185 whose expression was upregulated and downregulated, respectively), and 529 (248 and 281 whose expression was upregulated and downregulated, respectively) differentially expressed proteins (DEPs) were identified in T0d vs. T10d, T10d vs. T20d, and T0d vs. T20d comparison groups, respectively. Enrichment analysis showed that these DEPs were mainly involved in glutathione metabolism, carbon fixation, amino sugar and nucleotide sugar metabolism, biosynthesis of amino acids, photosynthesis, carbon metabolism, starch, and sucrose metabolism, galactose metabolism, protein processing and ribosomes. To further verify the proteomic data, the expression of corresponding genes that encode eight DEPs was confirmed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results of this study presented an important step toward understanding the resistance mechanisms of grapevine in response to waterlogging stress at the proteome level.

Morpho-Biometrical, Nutritional and Phytochemical Characterization of Carrot Landraces from Puglia Region (Southern Italy)

The explorations as a part of the regional BiodiverSO Programme of vegetable genetic resource rescue revealed that in the arenili (sandy shores) of “Salterns of Margherita di Savoia” (SMS), a coastal landscape area of Puglia region (southern Italy), along the commercial genotypes of small rooting species, landraces are still cultivated. The morpho-biometrical, nutritional and phytochemical properties of two carrot landraces (“Carota a punta lunga” and “Carota a punta tonda”) and a commercial carrot hybrid (“Presto”) collected from the SMS area are examined. The study highlighted that the pedological conditions of the arenili of the SMS area are the main driving force in controlling the nutritional and nutraceutical characteristics of carrot, conferring to genotypes grown in this area a high profile in comparison with literature data. In the site of cultivation of arenili, a large variability in the morpho-qualitative traits emerged among carrot genotypes. “Carota a punta tonda” stands for a promising genotype being very rich in phenols (209.8 mg kg−1 fw) (mainly di-caffeic acid derivative and chlorogenic acid), ß-carotene (21,512 µg 100 g−1 fw), and high antioxidative proprieties. “Carota a punta tonda” could be considered as a healthy product for consumers and also amenable to selection for breeding purpose. Increasing the knowledge about nutritional and nutraceutical properties of local landraces may push the preference of consumers beyond the local community and, at the same time, farmers can be stimulated to continue their cultivation. Thus, the promotion of their on-farm/in situ conservation (cultivation) could represent an efficient strategy for agro-biodiversity preservation.

How Does the Waterlogging Regime Affect Crop Yield? A Global Meta-Analysis

Waterlogging, an abiotic stress, severely restricts crop yield in various parts of the world. Thus, we conducted a meta-analysis of 2,419 comparisons from 115 studies to comprehensively evaluate the overall change in crop yield induced by waterlogging in the global region. The results suggested that waterlogging obviously decreased crop yield by 32.9% on average, compared with no waterlogging, which was a result of a reduced 1,000-grain weight (13.67%), biomass (28.89%), plant height (10.68%), net photosynthetic rate (P n , 39.04%), and leaf area index (LAI, 22.89%). The overall effect of a waterlogging regime on crop yield is related to the crop type; the crop yield reduction varied between wheat (25.53%) and cotton (59.95%), with an overall average value of 36.81% under field conditions. In addition, we also found that compared with no waterlogging, waterlogging in the reproductive growth stage (41.90%) caused a greater yield reduction than in the vegetative growth stage (34.75%). Furthermore, decreases in crop yield were observed with an extension in the waterlogging duration; the greatest decreases in crop yield occurred at 15 < D ≤ 28 (53.19 and 55.96%) under field and potted conditions, respectively. Overall, the results of this meta-analysis showed that waterlogging can decrease crop yield and was mainly affected by crop type, growth stage, and experimental duration.

Elevated temperature and waterlogging decrease cottonseed quality by altering the accumulation and distribution of carbohydrates, oil and protein

Soil waterlogging and high-temperature events have occurred simultaneously in recent years in the Yangtze River basin cotton belt region of China, negatively affecting the development and quality of cottonseed. This study investigated the effects of the combination of elevated temperature (ET) (34.1/29.0°C) and waterlogging (3 or 6 days) on the accumulation and distribution of oil, protein and carbohydrates in cottonseed during flowering and boll development. The results showed that ET resulted in greater decreases in cottonseed biomass under waterlogging than under control conditions. The combination of waterlogging and ET significantly limited the accumulation of carbohydrates and oil contents. However, ET promoted protein accumulation and compensated for the negative effects of 3-day waterlogging on the final protein content. The combined ET and 6-day waterlogging significantly decreased the final contents of oil and protein by limiting carbon flux and NADPH supply because of the decreased activities of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) and glucose-6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49). The PEPC activity was correlated more with protein content than oil content. In addition, simultaneous exposure to waterlogging and ET resulted in lower unsaturated fatty acid/saturated fatty acid ratios and essential amino acid/non-essential amino acid ratios than did exposure to the individual factors alone. These findings could provide the theoretical support for the prospective assessment of effects of high temperature and waterlogging stresses on cotton production under climate change, and they can help to develop effective techniques in cotton cultivation.

Response of soybean to soil waterlogging associated with iron excess in the reproductive stage

Soil waterlogging is a common problem in some agricultural areas, including regions under soybean (Glycine max) cultivation. In waterlogged soils, soil O₂ depletion occurs due to aerobic microorganisms and plants, affecting the metabolic and physiological processes of plants after suffering anoxia in their root tissue. Another harmful factor in this situation is the exponential increase in the availability of iron (Fe) in the soil, which may result in absorption of excess Fe. The present study sought to evaluate the response mechanisms in soybean leaves 'Agroeste 3680' by physiological and biochemical analyses associating them with the development of pods in non-waterlogged and waterlogged soil, combined with one moderate and two toxic levels of Fe. Gas exchange was strongly affected by soil waterlogging. Excess Fe without soil waterlogging reduced photosynthetic pigments, and potentiated this reduction when associated with soil waterlogging. Starch and ureide accumulation in the first newly expanded trifoliate leaves proved to be response mechanisms induced by soil waterlogging and excess Fe, since plants cultivated under soil non-waterlogged soil at 25 mg dm^-3 Fe showed lower contents when compared to stressed plants. Thus, starch and ureide accumulation could be considered efficient biomarkers of phytotoxicity caused by soil waterlogging and excess Fe in soybean plants. The reproductive development was abruptly interrupted by the imposition of stresses, leading to a loss of pod dry biomass, which was largely due to the substantial decrease in the net photosynthetic rate, as expressed by area (A), the blockage of carbohydrate transport to sink tissues and an increase of malondialdehyde (MDA). The negative effect on reproductive development was more pronounced under waterlogged soil.

A comparative proteomic analysis of engineered and bio synthesized silver nanoparticles on soybean seedlings

Nanoparticles (NPs) are synthesized by different methods and response mechanism of plants varied towards NPs based on their origin. To study the effects of bio synthesized (BS) and chemically synthesized (CS) silver NPs on soybean, a gel-free/ label-free proteomic technique was used. Length of root and hypocotyl was enhanced by BS compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to 1 and 50 ppm. A total of 190 and 173 differentially changed proteins were identified in BS and CS silver NPs treated soybean, respectively. Twenty proteins commonly changed between BS and CS silver NPs treated soybean. Differentially-changed proteins were associated with protein-degradation and stress according to functional categorization. From proteomics, abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs treated soybean. These results suggest that BS silver NPs enhanced the growth of soybean by regulating proteins related to protein-degradation and ATP contents, which are negatively affected by CS silver NPs. BIOLOGICAL SIGNIFICANCE: This study highlighted the response mechanism of soybean towards bio synthesized (BS) and chemically synthesized (CS) silver nanoparticles (NPs) using a gel-free/ label-free proteomics technique. Length of root and hypocotyl was enhanced by BS silver NPs compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to other concentrations. Differentially changed proteins were associated with protein degradation and stress. From the proteomics, the abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs compared to BS silver NPs treated soybean. These results suggest that the BS silver NPs enhanced the growth of soybean by regulating the proteins related to protein degradation and ATP contents, which are negatively affected by the CS silver NPs.

Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress

Submergence is one of the environmental stresses that limit plant growth and development. Dactylis glomerata L. is an important cool-season forage grass globally. To investigate the genes related to submergence response and the molecular mechanism associated with submergence tolerance, the transcriptome of D. glomerata in response to waterlogging treatment was analyzed. RNA-sequencing was performed in two D. glomerata cultivars, submergence tolerant 'Dianbei' and submergence sensitive 'Anba'. A total of 50,045 unique genes matched the known proteins in the NCBI nr database by BLAST searches and 60.8% (30,418) of these genes were annotated with GO terms. Among these, 1395 genes only differentially expressed in 'Dianbei' and 18 genes shown different expression all the time were detected between the submergence tolerant 'Dianbei' and sensitive 'Anba'. Gene ontology (GO) and KEGG pathway enrichment analyses demonstrated that the DEGs were mainly implicated in oxidation-reduction system, nucleic acid binding transcription factor activity, and glycerol kinase activity. The D. glomerata assembled transcriptome provided substantial molecular resource for further genomic analysis of forage grasses in response to submergence stress. The significant difference in expression of specific unigenes may account for waterlogging tolerance or acclimation in the two different D. glomerata cultivars. This study provided new insights into the molecular basis of submergence tolerance in D. glomerata.

Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions

Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.

Love on wings, a Dof family protein regulates floral vasculature in Vigna radiata

BACKGROUND

The interaction among plants and their pollinators has been a major factor which enriched floral traits known as pollination syndromes and promoted the diversification of flowering plants. One of the bee-pollination syndromes in Faboideae with keel blossoms is the formation of a landing platform by wing and keel petals. However, the molecular mechanisms of elaborating a keel blossom remain unclear.

RESULTS

By performing large scale mutagenesis, we isolated and characterized a mutant in Vigna radiata, love on wings (low), which shows developmental defects in petal asymmetry and vasculature, leading to a failure in landing platform formation. We cloned the locus through map-based cloning together with RNA-sequencing (RNA-seq) analysis. We found that LOW encoded a nucleus-localized Dof-like protein and was expressed in the flower provascular and vascular tissues. A single copy of LOW was detected in legumes, in contrast with other taxa where there seems to be at least 2 copies. Thirty one Dof proteins have been identified from the V. radiata's genome, which can be further divided into four Major Cluster of Orthologous Groups (MCOGs). We also showed that ectopic expression of LOW in Arabidopsis driven by its native promoter caused changes in petal vasculature pattern.

CONCLUSIONS

To summarize, our study isolated a legume Dof-like factor LOW from V. radiata, which affects vasculature development in this species and this change can, in turn, impact petal development and overall morphology of keel blossom.

Exploring Legume-Rhizobia Symbiotic Models for Waterlogging Tolerance

Unexpected and increasingly frequent extreme precipitation events result in soil flooding or waterlogging. Legumes have the capacity to establish a symbiotic relationship with endosymbiotic atmospheric dinitrogen-fixing rhizobia, thus contributing to natural nitrogen soil enrichment and reducing the need for chemical fertilization. The impact of waterlogging on nitrogen fixation and legume productivity needs to be considered for crop improvement. This review focuses on the legumes-rhizobia symbiotic models. We aim to summarize the mechanisms underlying symbiosis establishment, nodule development and functioning under waterlogging. The mechanisms of oxygen sensing of the host plant and symbiotic partner are considered in view of recent scientific advances.

Growth and nutrient content of Echinacea purpurea as affected by the combination of phosphorus with arbuscular mycorrhizal fungus and Pseudomonas florescent bacterium under different irrigation regimes

The excessive use of chemical fertilizers has caused many environmental problems and threatens the health of the human communities at the global level. However, the use of some beneficial soil microorganisms in addition to supplying nutrients to plants helps protect the environment. In order to achieve this goal, the effects of different irrigation regimes and application of phosphorus (P) fertilizer, with mycorrhizal arbuscular fungus (AMF) or Pseudomonas fluorescens bacterium (PFB), were studied on the growth and nutrients of Echinacea purpurea. The main factor included soil irrigation after 25, 50 and 75% of soil moisture depletion and a sub-factor of P supplied in six levels (100% chemical P, 50% P + AMF, AMF, 50% P + PFB, PFB and a control test without P fertilizer). Results showed that an increase in drought intensity reduced the absorption of nutrients and relative water content (RWC), while ion leakage increased in the leaf of E. purpurea. The AMF had a more clear effect on the N, Cu, Mn, and Fe, but PFB was more effective in an increase of Zn. With the use of PFB in the second harvest, the amount of leaf and root Zn was increased by 30.39% and 31.88%, respectively. Although 100% chemical P could increase more P concentration in the root, the combination of P fertilizer with AMF transferred more P from root to leaf. In the first and second harvest, a combination of P with PFB respectively increased the plant biological yield by 10.77% and 17.33% as compared to control. Vegetative traits, Mn, and Zn illustrated a significant increase in the second harvest. Finally, the results showed successful coexistence of bio-fertilizers with E. purpurea in increasing the content of nutrients, improving water absorption, and reducing the adverse effects of drought stress.

Mutualistic co-evolution of T3SSs during the establishment of symbiotic relationships between Vigna radiata and Bradyrhizobia

This study supports the idea that the evolution of type III secretion system (T3SS) is one of the factors that controls Vigna radiata-bradyrhizobia symbiosis. Based on phylogenetic tree data and gene arrangements, it seems that the T3SSs of the Thai bradyrhizobial strains SUTN9-2, DOA1, and DOA9 and the Senegalese strain ORS3257 may share the same origin. Therefore, strains SUTN9-2, DOA1, DOA9, and ORS3257 may have evolved their T3SSs independently from other bradyrhizobia, depending on biological and/or geological events. For functional analyses, the rhcJ genes of ORS3257, SUTN9-2, DOA9, and USDA110 were disrupted. These mutations had cultivar-specific effects on nodulation properties. The T3SSs of ORS3257 and DOA9 showed negative effects on V. radiata nodulation, while the T3SS of SUTN9-2 showed no effect on V. radiata symbiosis. In the roots of V. radiata CN72, the expression levels of the PR1 gene after inoculation with ORS3257 and DOA9 were significantly higher than those after inoculation with ORS3257 ΩT3SS, DOA9 ΩT3SS, and SUTN9-2. The T3Es from ORS3257 and DOA9 could trigger PR1 expression, which ultimately leads to abort nodulation. In contrast, the T3E from SUTN9-2 reduced PR1 expression. It seems that the mutualistic relationship between SUTN9-2 and V. radiata may have led to the selection of the most well-adapted combination of T3SS and symbiotic bradyrhizobial genotype.

Genetic control of compound leaf development in the mungbean (Vigna radiata L.)

Many studies suggest that there are distinct regulatory processes controlling compound leaf development in different clades of legumes. Loss of function of the LEAFY (LFY) orthologs results in a reduction of leaf complexity to different degrees in inverted repeat-lacking clade (IRLC) and non-IRLC species. To further understand the role of LFY orthologs and the molecular mechanism in compound leaf development in non-IRLC plants, we studied leaf development in unifoliate leaf (un) mutant, a classical mutant of mungbean (Vigna radiata L.), which showed a complete conversion of compound leaves into simple leaves. Our analysis revealed that UN encoded the mungbean LFY ortholog (VrLFY) and played a significant role in leaf development. In situ RNA hybridization results showed that STM-like KNOXI genes were expressed in compound leaf primordia in mungbean. Furthermore, increased leaflet number in heptafoliate leaflets1 (hel1) mutants was demonstrated to depend on the function of VrLFY and KNOXI genes in mungbean. Our results suggested that HEL1 is a key factor coordinating distinct processes in the control of compound leaf development in mungbean and its related non-IRLC legumes.

Possible interaction of ROS, antioxidants and ABA to survive osmotic stress upon acclimation in Vigna radiata L. Wilczek seedlings

Acclimation is a process of adjustment to gradual environmental change that enables plants to survive further stress by triggering some tolerance mechanism possibly involving ABA, ROS and oxidative metabolism. Here we have studied acclimation responses in terms of the performances with regard to physiological (growth and relative water content) and biochemical (chlorophyll, carotenoids, protein, malondialdehyde, sugar content) attributes, ABA production and stomatal sensitivity to exogenous ABA, extracellular ROS production and activation of antioxidant system. Our study reveals that repeated exposure to short-term mild water stress simulated by polyethylene glycol (PEG-6000) induces acclimation in mung bean (Vigna radiata L. Wilczek) seedlings. Acclimation induced tolerance was associated with reduced leaf size and enhanced root growth, accumulation of soluble sugar as osmoprotectant, maintenance of water potential, lessening of membrane damage as indicated by lower MDA content. Acclimated mung bean seedlings have shown greater degree of tolerance through increased production of and enhanced sensitivity to ABA (as reflected by faster stomatal closure), enhanced production of extracellular O₂^.- and H₂O₂ and the elevated activities of antioxidative enzymes to control the oxidative burst. Taken together, the results convey that acclimated seedlings minimize osmotic stress-induced damage through a possible network of ABA, ROS and antioxidants.

Effect of post-anthesis waterlogging on biosynthesis and granule size distribution of starch in wheat grains

Waterlogging is one of the most common abiotic stress types in wheat production in many rainy areas of the world. Two locally widely grown winter wheat (Triticum aestivum L. cv Yumai 34 and Yangmai 9) were subjected to post-anthesis waterlogging in a pot experiment to investigate the impacts of waterlogging on the starch synthesis and the physiochemical properties. Post-anthesis waterlogging significantly decreased grain weight and affected the content of starch components. Waterlogging down-regulated the activity and expression of genes encoding soluble starch synthase [SSS (EC 2.4.1.21)], while up-regulated those of the granule bound starch synthase I [GBSSI (EC:2.4.1.242)]. This further resulted in decreased amylopectin content and increased amylose content. Waterlogging also caused a reduction in the number of starch granules, while increased the mean diameter of starch granules in mature grains, which was mainly due to an increase in the volume frequency percent of the A-type starch granules. Waterlogging also lowered the peak viscosity and trough viscosity of starch, but did not affect the breakdown viscosity and peak time. We concluded that the modified expressions of the starch synthase encoding genes were responsible for the changed size distribution of starch granules, which finally affected the starch pasting properties of wheat growing under post-anthesis waterlogging conditions.

MaRAP2-4, a waterlogging-responsive ERF from Mentha, regulates bidirectional sugar transporter AtSWEET10 to modulate stress response in Arabidopsis

As waterlogging and successive events severely influence growth and development of economically important plants, we attempted to characterize the role of a waterlogging-responsive group I (A-6) ethylene response factor (MaRAP2-4) from Mentha arvensis. Waterlogging, ethylene and methyl jasmonate rapidly induced the expression of MaRAP2-4. MaRAP2-4 interacted with multiple cis-elements like dehydration response elements (DRE1/2), anoxia/jasmonic acid response element (JARE) and GCC box showing its involvement in multiple responses. MaRAP2-4 localizes in the nucleus and acts as a transcriptional activator. Truncation and internal deletion identified a 20 amino acids potential transactivation domain (PLPSSVDAKLEAICQSLAIN) in MaRAP2-4. MaRAP2-4 transgenic Arabidopsis showed enhanced waterlogging and subsequent oxidative stress tolerance. Microarray analysis revealed that within up-regulated genes 483, 212 and 132 promoters carry either single or multiple copies of DRE, JARE and GCC cis-element/s, respectively. Within these promoters, a large section belongs to carbohydrate metabolism/transport, including many SWEET transporters. Further analysis showed MaRAP2-4 specifically targets two positions in AtSWEEET10 promoter carrying DRE and/or GCC box that might regulate carbohydrate availability and waterlogging tolerance. These results demonstrate that MaRAP2-4 is a positive regulator of waterlogging tolerance, and as energy-consuming processes such as carbohydrate biosynthesis are reduced under waterlogging-induced hypoxia, sugar transport through SWEETs may be the primary option to make sugar available to the required tissue.

Global gene expression in cotton (Gossypium hirsutum L.) leaves to waterlogging stress

Cotton is sensitive to waterlogging stress, which usually results in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in cotton remain elusive. Cotton was grown in a rain-shelter and subjected to 0 (control)-, 10-, 15- and 20-d waterlogging at flowering stage. The fourth-leaves on the main-stem from the top were sampled and immediately frozen in liquid nitrogen for physiological measurement. Global gene transcription in the leaves of 15-d waterlogged plants was analyzed by RNA-Seq. Seven hundred and ninety four genes were up-regulated and 1018 genes were down-regulated in waterlogged cotton leaves compared with non-waterlogged control. The differentially expressed genes were mainly related to photosynthesis, nitrogen metabolism, starch and sucrose metabolism, glycolysis and plant hormone signal transduction. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that most genes related to flavonoid biosynthesis, oxidative phosphorylation, amino acid metabolism and biosynthesis as well as circadian rhythm pathways were differently expressed. Waterlogging increased the expression of anaerobic fermentation related genes, such as alcohol dehydrogenase (ADH), but decreased the leaf chlorophyll concentration and photosynthesis by down-regulating the expression of photosynthesis related genes. Many genes related to plant hormones and transcription factors were differently expressed under waterlogging stress. Most of the ethylene related genes and ethylene-responsive factor-type transcription factors were up-regulated under water-logging stress, suggesting that ethylene may play key roles in the survival of cotton under waterlogging stress.

Physiological and de novo transcriptome analysis of the fermentation mechanism of Cerasus sachalinensis roots in response to short-term waterlogging

Background

Cerasus sachalinensis is widely used in cool regions as a sweet cherry rootstock and is known for its sensitivity to soil waterlogging and waterlogging stress. However, the limited availability of Cerasus genomic resources has considerably restricted the exploration of its waterlogging response mechanism. To understand its reaction to short-term waterlogging, we analyzed the physiology and transcriptomes of C. sachalinensis roots in response to different waterlogging durations.

Results

In this study, 12,487 differentially expressed genes (DEGs) were identified from Cerasus sachalinensis roots under different waterlogging durations. Carbon metabolism and energy maintenance formed the first coping mechanism stage of C. sachalinensis in response to low oxygen conditions. Root energy processes, including root respiration and activities of the fermentation enzymes alcohol dehydrogenase, pyruvate decarboxylase, and lactate dehydrogenase, showed unique changes after 0 h, 3 h, 6 h, and 24 h of waterlogging exposure. Ribonucleic acid sequencing was used to analyze transcriptome changes in C. sachalinensis roots treated with 3 h, 6 h, and 24 h of waterlogging stress. After de novo assembly, 597,474 unigenes were recognized, of which 355,350 (59.47%) were annotated. To identify the most important pathways represented by DEGs, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to compare these genes. The first stage of root reaction to waterlogging stress was activation of carbohydrate metabolism to produce more glucose and maintain energy levels. At 3 h, the glycolytic and fermentation pathways were activated to maintain adenosine triphosphate production. At 24 h, pathways involved in the translation of proteins were activated to further assist the plant in tolerating waterlogging stress. These findings will facilitate a further understanding of the potential mechanisms of plant responses to waterlogging at physiological and transcriptome levels.

Conclusions

Carbon metabolism and energy maintenance formed the first coping mechanism C. sachalinensis in response to low oxygen conditions, and they may be responsible for its short-term waterlogging response. Our study not only provides the assessment of genomic resources of Cerasus but also paves the way for probing the metabolic and molecular mechanisms underlying the short-term waterlogging response in C. sachalinensis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4055-1) contains supplementary material, which is available to authorized users.

Proteomic Analysis of Calcium Effects on Soybean Root Tip under Flooding and Drought Stresses

Flooding and drought are disadvantageous environmental conditions that induce cytosolic calcium in soybean. To explore the effects of flooding- and drought-induced increases in calcium, a gel-free/label-free proteomic analysis was performed. Cytosolic calcium was decreased by blocking calcium channels in the endoplasmic reticulum (ER) and plasma membrane under both stresses. Calnexin, protein disulfide isomerase, heat shock proteins and thioredoxin were predominantly affected as the ER proteins in response to calcium, and ER-associated degradation-related proteins of HCP-like superfamily protein were up-regulated under stress exposure and then down-regulated. Glycolysis, fermentation, the tricarboxylic acid cycle and amino acid metabolism were mainly induced as the types of cellular metabolism in response to calcium under both stresses. Pyruvate decarboxylase was increased and decreased under flooding and drought, respectively, and was further decreased by the reduction of cytosolic calcium; however, it was recovered by exogenous calcium under both stresses. Furthermore, pyruvate decarboxylase activity was increased under flooding, but decreased under drought. These results suggest that calcium is involved in protein folding in the ER, and ER-associated degradation might alleviate ER stress during the early stage of both stresses. Furthermore, calcium appears to modify energy metabolism, and pyruvate decarboxylase may be a key enzyme in this process under flooding and drought.

Sex-specific responses to winter flooding, spring waterlogging and post-flooding recovery in Populus deltoides

Winter flooding events are common in some rivers and streams due to dam constructions, and flooding and waterlogging inhibit the growth of trees in riparian zones. This study investigated sex-specific morphological, physiological and ultrastructural responses to various durations of winter flooding and spring waterlogging stresses, and post-flooding recovery characteristics in Populus deltoides. There were no significant differences in the morphological, ultrastructural and the majority of physiological traits in trees subjected to medium and severe winter flooding stresses, suggesting that males and females of P. deltoides were winter flooding tolerant, and insensitive to winter flooding duration. Males were more tolerant to winter flooding stress in terms of photosynthesis and chlorophyll fluorescence than females. Females displayed greater oxidative damage due to flooding stress than males. Males developed more efficient antioxidant enzymatic systems to control reactive oxygen species. Both sexes had similarly strong post-flooding recovery capabilities in terms of plant growth, and physiological and ultrastructural parameters. However, Males had better recovery capabilities in terms of pigment content. These results increase the understanding of poplars's adaptation to winter flooding stress. They also elucidate sex-specific differences in response to flooding stress during the dormant season, and during post-flooding recovery periods.

Cellulose Anionic Hydrogels Based on Cellulose Nanofibers As Natural Stimulants for Seed Germination and Seedling Growth

Cellulose anionic hydrogels were successfully prepared by dissolving TEMPO-oxidized cellulose nanofibers in NaOH/urea aqueous solution and being cross-linked with epichlorohydrin. The hydrogels exhibited microporous structure and high hydrophilicity, which contribute to the excellent water absorption property. The growth indexes, including the germination rate, root length, shoot length, fresh weight, and dry weight of the seedlings, were investigated. The results showed that cellulose anionic hydrogels with suitable carboxylate contents as plant growth regulators could be beneficial for seed germination and growth. Moreover, they presented preferable antifungal activity during the breeding and growth of the sesame seed breeding. Thus, the cellulose anionic hydrogels with suitable carboxylate contents could be applied as soilless culture mediums for plant growth. This research provided a simple and effective method for the fabrication of cellulose anionic hydrogel and evaluated its application in agriculture.

Insights into the Response of Soybean Mitochondrial Proteins to Various Sizes of Aluminum Oxide Nanoparticles under Flooding Stress

Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. For possible interactions between NPs and crops under flooding stress to be investigated, the molecular mechanisms in soybeans affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of the root including hypocotyl was increased, and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway. Hierarchical clustering analysis indicated that ribosomal proteins were also increased upon exposure to flooding-stressed plants with 30-60 nm Al2O3 NPs. Mitochondrion was the target organelle of Al2O3 NPs under flooding-stress conditions. Mitochondrial proteomic analysis revealed that the abundance of voltage-dependent anion channel protein was increased upon exposure to flooding-stressed soybeans with 135 nm Al2O3 NPs, indicating the permeability of the mitochondrial membrane was increased. Furthermore, isocitrate dehydrogenase was increased upon exposure of plants to 5 nm Al2O3 NPs under flooding conditions. These results suggest that Al2O3 NPs of various sizes affect mitochondrial proteins under flooding stress by regulating membrane permeability and tricarboxylic acid cycle activity.

Overexpression of Actinidia deliciosa pyruvate decarboxylase 1 gene enhances waterlogging stress in transgenic Arabidopsis thaliana

Ethanolic fermentation is classically associated with waterlogging tolerance when plant cells switch from respiration to anaerobic fermentation. Pyruvate decarboxylase (PDC), which catalyzes the first step in this pathway, is thought to be the main regulatory enzyme. Here, we cloned a full-length PDC cDNA sequence from kiwifruit, named AdPDC1. We determined the expression of the AdPDC1 gene in kiwifruit under different environmental stresses using qRT-PCR, and the results showed that the increase of AdPDC1 expression during waterlogging stress was much higher than that during salt, cold, heat and drought stresses. Overexpression of kiwifruit AdPDC1 in transgenic Arabidopsis enhanced the resistance to waterlogging stress but could not enhance resistance to cold stress at five weeks old seedlings. Overexpression of kiwifruit AdPDC1 in transgenic Arabidopsis could not enhance resistance to NaCl and mannitol stresses at the stage of seed germination and in early seedlings. These results suggested that the kiwifruit AdPDC1 gene is required during waterlogging but might not be required during other environmental stresses. Expression of the AdPDC1 gene was down-regulated by abscisic acid (ABA) in kiwifruit, and overexpression of the AdPDC1 gene in Arabidopsis inhibited seed germination and root length under ABA treatment, indicating that ABA might negatively regulate the AdPDC1 gene under waterlogging stress.

Quantitative proteomic analysis of post-flooding recovery in soybean root exposed to aluminum oxide nanoparticles

Aluminum oxide nanoparticles (Al2O3 NPs) are used in various commercial and agricultural products. Soybean exhibits severe reduction in growth under flooding condition. To examine the effects of Al2O3 NPs on the recovery of soybean from flooding, proteomic analysis was performed. Survival percentage and weight/length of root including hypocotyl were improved after 2 and 4days of flooding with 50ppm Al2O3 NPs leading to recovery as compared to flooding. A total of 211 common proteins were changed in abundance during the recovery period after treatment without or with Al2O3 NPs. These proteins were related to protein synthesis, stress, cell wall, and signaling. Among the identified stress-related proteins, S-adenosyl-l-methionine dependent methyltransferases were recovered from flooding with Al2O3 NPs. Hierarchical clustering divided the identified proteins into three clusters. Cluster II exhibited the greatest change in proteins related to protein synthesis, transport, and development during the recovery from flooding with Al2O3 NPs. However, activity of enolase remained unchanged during flooding leading to subsequent recovery with Al2O3 NPs. These results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase might be involved in mediating recovery responses by Al2O3 NPs.

BIOLOGICAL SIGNIFICANCE

This study highlighted the role of Al2O3 NPs in recovery of soybean seedlings from flooding stress using gel-free proteomic technique. The key findings of this study are as follows: (i) survival percentage was enhanced at 50ppm Al2O3 NPs during the recovery stage; (ii) seedling weight and weight/length of root including hypocotyl improved at 50ppm Al2O3 NPs during the period of recovery; (iii) protein synthesis and stress related proteins were increased on recovery after flooding without or with Al2O3 NPs; (iv) the abundance of S-adenosyl-l-methionine dependent methyltransferases recovered from flooding with Al2O3 NPs; (v) glycolysis related proteins amplified under flooding with Al2O3 NPs; (vi) enolase enzyme remained unchanged during flooding leading to subsequent recovery from flooding with Al2O3 NPs. Collectively, these results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase are involved in response to flooding with Al2O3 NPs and might be helpful in recovery from flooding stress.

ALA Pretreatment Improves Waterlogging Tolerance of Fig Plants

5-aminolevulinic acid (ALA), a natural and environmentally friendly plant growth regulator, can improve plant tolerance to various environmental stresses. However, whether ALA can improve plant waterlogging tolerance is unknown. Here, we investigated the effects of ALA pretreatment on the waterlogging-induced damage of fig (Ficus carica Linn.) plants, which often suffer from waterlogging stress. ALA pretreatment significantly alleviated stress-induced morphological damage, increased leaf relative water content (RWC), and reduced leaf superoxide anion ([Formula: see text]) production rate and malonaldehyde (MDA) content in fig leaves, indicating ALA mitigates waterlogging stress of fig plants. We further demonstrated that ALA pretreatment largely promoted leaf chlorophyll content, photosynthetic electron transfer ability, and photosynthetic performance index, indicating ALA significantly improves plant photosynthetic efficiency under waterlogging stress. Moreover, ALA pretreatment significantly increased activities of leaf superoxide dismutase (SOD) and peroxidase (POD), root vigor, and activities of root alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH), indicating ALA also significantly improves antioxidant ability and root function of fig plants under waterlogging stress. Taken together, ALA pretreatment improves waterlogging tolerance of fig plants significantly, and the promoted root respiration, leaf photosynthesis, and antioxidant ability may contribute greatly to this improvement. Our data firstly shows that ALA can improve plant waterlogging tolerance.

Comparative Proteomic Analysis Provides Insight into the Key Proteins Involved in Cucumber (Cucumis sativus L.) Adventitious Root Emergence under Waterlogging Stress

Waterlogging is a common abiotic stress in both natural and agricultural systems, and it primarily affects plant growth by the slow oxygen diffusion in water. To sustain root function in the hypoxic environment, a key adaptation for waterlogging tolerant plants is the formation of adventitious roots (ARs). We found that cucumber waterlogging tolerant line Zaoer-N seedlings adapt to waterlogging stress by developing a larger number of ARs in hypocotyls, while almost no AR is generated in sensitive line Pepino. To understand the molecular mechanisms underlying AR emergence, the iTRAQ-based quantitative proteomics approach was employed to map the proteomes of hypocotyls cells of the Zaoer-N and Pepino under control and waterlogging conditions. A total of 5508 proteins were identified and 146 were differentially regulated proteins (DRPs), of which 47 and 56 DRPs were specific to tolerant and sensitive line, respectively. In the waterlogged Zaoer-N hypocotyls, DRPs related to alcohol dehydrogenases (ADH), 1-aminocyclopropane-1-carboxylicacid oxidases, peroxidases, 60S ribosomal proteins, GSDL esterases/lipases, histone deacetylases, and histone H5 and were strongly overrepresented to manage the energy crisis, promote ethylene release, minimize oxidative damage, mobilize storage lipids, and stimulate cell division, differentiation and growth. The evaluations of ethylene production, ADH activity, pyruvate decarboxylase (PDC) activity and ethanol production were in good agreement with the proteomic results. qRT-PCR analysis of the corresponding 146 genes further confirmed the accuracy of the observed protein abundance. These findings shed light on the mechanisms underlying waterlogging triggered cucumber ARs emergence, and provided valuable information for the breeding of cucumber with enhanced tolerance to waterlogging.

Proteomic analysis of flooded soybean root exposed to aluminum oxide nanoparticles

Aluminum oxide (Al2O3) nanoparticles are used in agricultural products and cause various adverse growth effects on different plant species. To study the effects of Al2O3 nanoparticles on soybean under flooding stress, a gel-free proteomic technique was used. Morphological analysis revealed that treatment with 50 ppm Al2O3 nanoparticles under flooding stress enhanced soybean growth compared to ZnO and Ag nanoparticles. A total of 172 common proteins that significantly changed in abundance among control, flooding-stressed, and flooding-stressed soybean treated with Al2O3 nanoparticles were mainly related to energy metabolism. Under Al2O3 nanoparticles the energy metabolism was decreased compared to flooding stress. Hierarchical clustering divided identified proteins into four clusters, with proteins related to glycolysis exhibiting the greatest changes in abundance. Al2O3 nanoparticle-responsive proteins were predominantly related to protein synthesis/degradation, glycolysis, and lipid metabolism. mRNA expression analysis of Al2O3 nanoparticle-responsive proteins that displayed a 5-fold change in abundance revealed that NmrA-like negative transcriptional regulator was up-regulated, and flavodoxin-like quinone reductase was down-regulated. Moreover, cell death in root including hypocotyl was less evident in flooding-stressed with Al2O3 nanoparticles compared to flooding-treated soybean. These results suggest that Al2O3 nanoparticles might promote the growth of soybean under flooding stress by regulating energy metabolism and cell death.

Early physiological flood tolerance is followed by slow post-flooding root recovery in the dryland riparian tree Eucalyptus camaldulensis subsp. refulgens

We investigated physiological and morphological responses to flooding and recovery in Eucalyptus camaldulensis subsp. refulgens, a riparian tree species from a dryland region prone to intense episodic floods. Seedlings in soil flooded for 88 d produced extensive adventitious roots, displayed stem hypertrophy (stem diameter increased by 93%) and increased root porosity owing to aerenchyma formation. Net photosynthesis (Pn) and stomatal conductance (gs) were maintained for at least 2 weeks of soil flooding, contrasting with previous studies of other subspecies of E. camaldulensis. Gradual declines followed in both gs (30% less than controls) and Pn (19% less). Total leaf soluble sugars did not differ between flooded and control plants. Root mass did not recover 32 d after flooding ceased, but gs was not lower than controls, suggesting the root system was able to functionally compensate. However, the limited root growth during recovery after flooding was surprising given the importance of extensive root systems in dryland environments. We conclude that early flood tolerance could be an adaptation to capitalize on scarce water resources in a water-limited environment. Overall, our findings highlight the need to assess flooding responses in relation to a species' fitness for particular flood regimes or ecological niches.

Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation

Glycosyltransferases play diverse roles in cellular metabolism by modifying the activities of regulatory metabolites. Three stress-regulated UDP-glucosyltransferase-encoding genes have been isolated from the stigmas of saffron, UGT85U1, UGT85U2 and UGT85V1, which belong to the UGT85 family that includes members associated with stress responses and cell cycle regulation. Arabidopsis constitutively expressing UGT85U1 exhibited and increased anchor root development. No differences were observed in the timing of root emergence, in leaf, stem and flower morphology or flowering time. However, salt and oxidative stress tolerance was enhanced in these plants. Levels of glycosylated compounds were measured in these plants and showed changes in the composition of several indole-derivatives. Moreover, auxin levels in the roots were higher compared to wild type. The expression of several key genes related to root development and auxin homeostasis, including CDKB2.1, CDKB2.2, PIN2, 3 and 4; TIR1, SHR, and CYCD6, were differentially regulated with an increase of expression level of SHR, CYCD6, CDKB2.1 and PIN2. The obtained results showed that UGT85U1 takes part in root growth regulation via auxin signal alteration and the modified expression of cell cycle-related genes, resulting in significantly improved survival during oxidative and salt stress treatments.

Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress

Flooding stress causes growth inhibition and ultimately death in most crop species by limiting of energy production. To better understand plant responses to flooding stress, here, flooding-responsive proteins in the cotyledons of soybean were identified using a gel-free quantitative proteomic approach. One hundred forty six proteins were commonly observed in both control and flooding-stressed plants, and 19 were identified under only flooding stress conditions. The main functional categories were protein and development-related proteins. Protein-protein interaction analysis revealed that zincin-like metalloprotease and cupin family proteins were found to highly interact with other proteins under flooding stress. Plant stearoyl acyl-carrier protein, ascorbate peroxidase 1, and secretion-associated RAS superfamily 2 were down-regulated, whereas ferretin 1 was up-regulated at the transcription level. Notably, the levels of all corresponding proteins were decreased, indicating that mRNA translation to proteins is impaired under flooding conditions. Decreased levels of ferritin may lead to a strong deregulation of the expression of several metal transporter genes and over-accumulation of iron, which led to increased levels of reactive oxygen species, resulting to detoxification of these reactive species. Taken together, these results suggest that ferritin might have an essential role in protecting plant cells against oxidative damage under flooding conditions.

BIOLOGICAL SIGNIFICANCE

This study reported the comparative proteomic analysis of cotyledon of soybean plants between non-flooding and flooding conditions using the gel-free quantitative techniques. Mass spectrometry analysis of the proteins from cotyledon resulted in the identification of a total of 165 proteins under flooding stress. These proteins were assigned to different functional categories, such as protein, development, stress, redox, and glycolysis. Therefore, this study provides not only the comparative proteomic analysis but also the molecular mechanism underlying the flooding responsive protein functions in the cotyledon.

Analysis of gene expression and proteomic profiles of clonal genotypes from Theobroma cacao subjected to soil flooding

Soil flooding causes changes in gene transcription, synthesis and degradation of proteins and cell metabolism. The main objective of this study was to understand the biological events of Theobroma cacao during soil flooding-induced stress, using the analyses of gene expression and activity of key enzymes involved in fermentation, as well as the identification of differentially expressed proteins by mass spectrometry in two contrasting genotypes for flooding tolerance (tolerant - TSA-792 and susceptible - TSH-774). Soil anoxia caused by flooding has led to changes in the expression pattern of genes associated with the biosynthesis of alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC) and lactate dehydrogenase (LDH) in leaves and roots of the two evaluated genotypes. Significant differences were observed between the enzyme activities of the two genotypes. Leaves and roots of the TSA-792 genotype showed higher ADH activity as compared to the TSH-774 genotype, whereas the activities of PDC and LDH have varied over the 96 h of soil flooding, being higher for TSA-792 genotype, at the initial stage, and TSH-774 genotype, at the final stage. Some of the identified proteins are those typical of the anaerobic metabolism-involved in glycolysis and alcoholic fermentation-and different proteins associated with photosynthesis, protein metabolism and oxidative stress. The ability to maintain glycolysis and induce fermentation was observed to play an important role in anoxia tolerance in cacao and may also serve to distinguish tolerant and susceptible genotypes in relation to this stressor.

Alterations in Soluble Class III Peroxidases of Maize Shoots by Flooding Stress

Due to changing climate, flooding (waterlogged soils and submergence) becomes a major problem in agriculture and crop production. In the present study, the effect of waterlogging was investigated on peroxidases of maize (Zea mays L.) leaves. The plants showed typical adaptations to flooding stress, i.e., alterations in chlorophyll a/b ratios and increased basal shoot diameter. Seven peroxidase bands could be detected by first dimension modified SDS-PAGE and 10 bands by first dimension high resolution Clear Native Electrophoresis that altered in dependence on plant development and time of waterlogging. Native isoelectric focusing revealed three acidic to neutral and four alkaline guaiacol peroxidases that could be further separated by high resolution Clear Native Electrophorese in the second dimension. One neutral peroxidase (pI 7.0) appeared to be down-regulated within four hours after flooding, whereas alkaline peroxidases (pI 9.2, 8.0 and 7.8) were up-regulated after 28 or 52 h. Second dimensions revealed molecular masses of 133 kDa and 85 kDa for peroxidases at pI 8.0 and 7.8, respectively. Size exclusion chromatography revealed native molecular masses of 30-58 kDa for peroxidases identified as class III peroxidases and ascorbate peroxidases by mass spectrometry. Possible functions of these peroxidases in flooding stress will be discussed.

Waterlogging during flowering and boll forming stages affects sucrose metabolism in the leaves subtending the cotton boll and its relationship with boll weight

The work explored sucrose metabolism in the leaves subtending the cotton boll (SBL) and its role in boll weight after waterlogging in cotton. Results showed that net photosynthesis rate (Pn), relative water content, contents of Chlorophyll a and Chlorophyll b, initial ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) activity and cytosolic fructose-1, 6-bisphosphatase (cy-FBPase) activity decreased with waterlogging in the SBL on fruiting branches 2-3 (FB2-3) and FB6-7. Activities of sucrose synthase (SuSy) and sucrose phosphate synthase (SPS) increased to the maximum up to 6 days of waterlogging then decreased with prolonged waterlogging. Rubisco activation and specific leaf weight increased and gene expressions of SuSy, SPS and rubisco activase (RCA) were all up-regulated with the duration of waterlogging, especially for the SBL on FB6-7. The induction of activity and gene expression of SuSy was most significant indicating its crucial role in sucrose metabolism after waterlogging. For the SBL in the later period of boll development on upper FB10-11 and FB14-15, the pattern seemed opposite to that of FB2-3 and FB6c7 as compensation effect in vegetative growth existed. Correlation analysis revealed that initial Rubisco activity and cy-FBPase activity were the main limitation to Pn reduction after waterlogging. Reduction in Pn, sucrose transformation rate and initial Rubisco activity directly decrease boll weight in waterlogged cotton. Besides the role in sucrose metabolism after waterlogging, SuSy also had a positive significant correlation with the duration of rapid-accumulation period for seed fiber weight (P<0.05). These findings elucidated mechanisms to waterlogging that affected seed fiber weight, which resulted from alteration in carbohydrates, enzymes and genes.

Waterlogging and nitric oxide induce gene expression and increase antioxidant enzyme activity in wheat (Triticum aestivum L.)

The effects of waterlogging (WL) and WL plus nitric oxide (WL+NO) were investigated in seedlings of one wheat cultivars (Triticum aestivum cv. Dogankent) and one wheat line (Triticum aestivum cv. Ducula-4). Under WL conditions, catalase activity was greater in Ducula-4 than in Dogankent. Glutathione reductase activity increased in Ducula-4 seedlings under WL+NO conditions, especially at 48 and 72 hours of treatment. Myb2 expression increased during the early hours of treatment in both wheat varieties exposed to WL, with 40-fold higher levels in Ducula-4, gradually decreasing to control levels. Under WL+NO treatment, Myb2 expression increased 44-fold at 12 hours and high levels of expression were still observed at 72 hours. When Ducula-4 seedlings were subjected to WL+NO treatment, PDPK expression increased approximately 15-fold at 3 hours and decreased to control levels at 72 hours. Under the same conditions, SST1 expression increased 3-fold at 3 and 12 hours and reached control levels during the subsequent hours. Among the genes studied, the highest level of expression was observed for Myb2. Moreover, gene expression was altered most by waterlogging in Ducula-4 seedlings.

Isolation of an alcohol dehydrogenase cDNA from and characterization of its expression in chrysanthemum under waterlogging

A PCR strategy was used to isolate a full-length CgADH (alcohol dehydrogenase) cDNA from chrysanthemum. The gene putatively encodes a 378 residue polypeptides, which shares 95% homology with tomato alcohol dehydrogenase class III. Endogenous ethylene generated in waterlogged Chrysanthemum zawadskii was enhanced by exogenous ethylene but decreased by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action. In waterlogged roots, the transcription of the gene encoding alcohol dehydrogenase (ADH, EC 1.1.1.1) increased rapidly but transiently, peaking at 7.5 fold the non-waterlogged level after 2h of stress. Waterlogging elevated ADH activity after a prolonged episode of stress. The exogenous supply of 40μLL(-1) ethylene suppressed the production of ethanol, while that of 4μLL(-1) 1-MCP enhanced it. Ethylene appeared to suppress an acceleration of both CgADH expression and fermentation, and alleviates ethanolic fermentation probably through by as a signal to acceleration of waterlogging-induced aerenchyma formation. This supports the previously observed phenomenon that the expression level of ADH gene is regulated by the local level of physiologically active ethylene. The relevance of the CgADH gene in relation to chrysanthemum waterlogging was discussed as well.

Low oxygen response mechanisms in green organisms

Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.

RAP2.6L overexpression delays waterlogging induced premature senescence by increasing stomatal closure more than antioxidant enzyme activity

Waterlogging usually results from overuse or poor management of irrigation water and is a serious constraint due to its damaging effects. RAP2.6L (At5g13330) overexpression enhances plant resistance to jasmonic acid, salicylic acid, abscisic acid (ABA) and ethylene in Arabidopsis thaliana. However, it is not known whether RAP2.6L overexpression in vivo improves plant tolerance to waterlogging stress. In this study, the RAP2.6L transcript was induced by waterlogging or an ABA treatment, which was reduced after pretreatment with an ABA biosynthesis inhibitor tungstate. Water loss and membrane leakage were reduced in RAP2.6L overexpression plants under waterlogging stress. Time course analyses of ABA content and production of hydrogen peroxide (H(2)O(2)) showed that increased ABA precedes the increase of H(2)O(2). It is also followed by a marked increase in the antioxidant enzyme activities. Increased ABA promoted stomatal closure and made leaves exhibit a delayed waterlogging induced premature senescence. Furthermore, RAP2.6L overexpression caused significant increases in the transcripts of antioxidant enzyme genes APX1 (ascorbate peroxidase 1) and FSD1 (Fe-superoxide dismutase 1), the ABA biosynthesis gene ABA1 (ABA deficient 1) and signaling gene ABH1 (ABA-hypersensitive 1) and the waterlogging responsive gene ADH1 (alcohol dehydrogenase 1), while the transcript of ABI1 (ABA insensitive 1) was decreased. ABA inhibits seed germination and seedling growth and phenotype analysis showed that the integration of abi1-1 mutation into the RAP2.6L overexpression lines reduces ABA sensitivity. These suggest that RAP2.6L overexpression delays waterlogging induced premature senescence and might function through ABI1-mediated ABA signaling pathway.