Evolution and mechanisms of plant tolerance to flooding stress

Ethylene enhanced waterlogging tolerance by changing root architecture and inducing aerenchyma formation in maize seedlings

Waterlogging negatively affects maize growth and yield. In this study, we found that ethylene played a vital role in plant adaptation to waterlogging. ET promotes better growth in seedlings under waterlogging conditions by altering root architecture and increasing lateral root formation by 42.1%. What's more, plants with high endogenous ethylene levels exhibited reduced sensitivity to waterlogging stress. ET also induced the formation of aerenchyma, a specialized tissue that facilitates gas exchange, in a different pattern compared to aerenchyma formed under waterlogging. Aerenchyma induced by ET was mainly located in the medial cortex of the roots and was not prone to decay. ethylene inhibited root elongation under normal conditions, but this inhibition was not alleviated under waterlogging stress. Upon activation of the ET signaling pathway, the transcription factor EREB90 promoted aerenchyma formation by enhancing the programmed cell death process. Overexpression of EREB90 resulted in increased waterlogging tolerance compared to wild type plants. Our findings suggest that pre-treatment of maize seedlings with ET before waterlogging stress can trigger the programmed cell death process and induce aerenchyma formation, thus improving waterlogging resistance.

iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions

Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.

Genetic Dissection of Extreme Seed-Flooding Tolerance in a Wild Soybean PI342618B by Linkage Mapping and Candidate Gene Analysis

Seed-flooding stress is one of major abiotic constraints that adversely affects soybean production worldwide. Identifying tolerant germplasms and revealing the genetic basis of seed-flooding tolerance are imperative goals for soybean breeding. In the present study, high-density linkage maps of two inter-specific recombinant inbred line (RIL) populations, named NJIRNP and NJIR4P, were utilized to identify major quantitative trait loci (QTLs) for seed-flooding tolerance using three parameters viz., germination rate (GR), normal seedling rate (NSR), and electrical conductivity (EC). A total of 25 and 18 QTLs were detected by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 12 common QTLs were identified through both methods. All favorable alleles for the tolerance are notably from the wild soybean parent. Moreover, four digenic epistatic QTL pairs were identified, and three of them showed no main effects. In addition, the pigmented soybean genotypes exhibited high seed-flooding tolerance compared with yellow seed coat genotypes in both populations. Moreover, out of five identified QTLs, one major region containing multiple QTLs associated with all three traits was identified on Chromosome 8, and most of the QTLs within this hotspot were major loci (R² > 10) and detectable in both populations and multiple environments. Based on the gene expression and functional annotation information, 10 candidate genes from QTL "hotspot 8-2" were screened for further analysis. Furthermore, the results of qRT-PCR and sequence analysis revealed that only one gene, GmDREB2 (Glyma.08G137600), was significantly induced under flooding stress and displayed a TTC tribasic insertion mutation of the nucleotide sequence in the tolerant wild parent (PI342618B). GmDREB2 encodes an ERF transcription factor, and the subcellular localization analysis using green fluorescent protein (GFP) revealed that GmDREB2 protein was localized in the nucleus and plasma membrane. Furthermore, overexpression of GmDREB2 significantly promoted the growth of soybean hairy roots, which might indicate its critical role in seed-flooding stress. Thus, GmDREB2 was considered as the most possible candidate gene for seed-flooding tolerance.

Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean

Soybean is highly sensitive to flooding and extreme rainfall. The phenotypic variation of flooding tolerance is a complex quantitative trait controlled by many genes and their interaction with environmental factors. We previously constructed a gene-pool relevant to soybean flooding-tolerant responses from integrated multiple omics and non-omics databases, and selected 144 prioritized flooding tolerance genes (FTgenes). In this study, we proposed a comprehensive framework at the systems level, using competitive (hypergeometric test) and self-contained (sum-statistic, sum-square-statistic) pathway-based approaches to identify biologically enriched pathways through evaluating the joint effects of the FTgenes within annotated pathways. These FTgenes were significantly enriched in 36 pathways in the Gene Ontology database. These pathways were related to plant hormones, defense-related, primary metabolic process, and system development pathways, which plays key roles in soybean flooding-induced responses. We further identified nine key FTgenes from important subnetworks extracted from several gene networks of enriched pathways. The nine key FTgenes were significantly expressed in soybean root under flooding stress in a qRT-PCR analysis. We demonstrated that this systems biology framework is promising to uncover important key genes underlying the molecular mechanisms of flooding-tolerant responses in soybean. This result supplied a good foundation for gene function analysis in further work.

Proline, a multifaceted signalling molecule in plant responses to abiotic stress: understanding the physiological mechanisms

Abiotic stresses have a detrimental impact on plant growth and productivity and are a major threat to sustainable crop production in rapidly changing environments. Proline, an important amino acid, plays an important role in maintaining the metabolism and growth of plants under abiotic stress conditions. Many insights indicate a positive relationship between proline accumulation and tolerance of plants to various abiotic stresses. Because of its metal chelator properties, it acts as a molecular chaperone, an antioxidative defence molecule that scavenges reactive oxygen species (ROS), as well as having signalling behaviour to activate specific gene functions that are crucial for plant recovery from stresses. It also acts as an osmoprotectant, a potential source to acquire nitrogen as well as carbon, and plays a significant role in the flowering and development of plants. Overproduction of proline in plant cells contributes to maintaining cellular homeostasis, water uptake, osmotic adjustment and redox balance to restore the cell structures and mitigate oxidative damage. Many reports reveal that transgenic plants, particularly those overexpressing genes tailored for proline accumulation, exhibit better adaptation to abiotic stresses. Therefore, this review aims to provide a comprehensive update on proline biosynthesis and accumulation in plants and its putative regulatory roles in mediating plant defence against abiotic stresses. Additionally, the current and future directions in research concerning manipulation of proline to induce gene functions that appear promising in genetics and genomics approaches to improve plant adaptive responses under changing climate conditions are also highlighted.

Cacao (Theobroma cacao L.) Response to Water Stress: Physiological Characterization and Antioxidant Gene Expression Profiling in Commercial Clones

The increase in events associated with drought constraints plant growth and crop performance. Cacao (Theobroma cacao L.) is sensitive to water deficit stress (DS), which limits productivity. The aim of this research was to characterise the response of seven (CCN51, FEAR5, ICS1, ICS60, ICS95, EET8, and TSH565) commercially important cacao clones to severe and temporal water deficit stress. Ten-month-old cacao trees were submitted to two treatments: well-watered and water-stressed until the leaf water potential (Ψ leaf) reached values between -3.0 and -3.5 MPa. The effects of hydric stress on water relations, gas exchange, photochemical activity, membrane integrity and oxidative stress-related gene expression were evaluated. All clones showed decreases in Ψ leaf, but TSH565 had a higher capacity to maintain water homeostasis in leaves. An initial response phase consisted of stomatal closure, a general mechanism to limit water loss: as a consequence, the photosynthetic rate dropped by approximately 98% on average. In some clones, the photosynthetic rate reached negative values at the maximum stress level, evidencing photorespiration and was confirmed by increased intracellular CO2. A second and photosynthetically limited phase was characterized by a drop in PSII quantum efficiency, which affected all clones. On average, all clones were able to recover after 4 days of rewatering. Water deficit triggered oxidative stress at the early phase, as evidenced by the upregulation of oxidative stress markers and genes encoding ROS scavenging enzymes. The effects of water deficit stress on energy metabolism were deduced given the upregulation of fermentative enzyme-coding genes. Altogether, our results suggest that the EET8 clone was the highest performing under water deficit while the ICS-60 clone was more susceptible to water stress. Importantly, the activation of the antioxidant system and PSII repair mechanism seem to play key roles in the observed differences in tolerance to water deficit stress among clones.

Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.

Source of Oxygen Fed to Adventitious Roots of Syzygium kunstleri (King) Bahadur and R.C. Gaur Grown in Hypoxic Conditions

Syzygium kunstleri, a woody plant species, adapts to hypoxic conditions by developing new adventitious roots. Here, we investigate its morphological adaptation to long-term water level changes and the sources and pathways of O₂ supplied to its adventitious roots. Cuttings were cultivated in hydroponic and agar media, and then, the water level was increased by 6 cm following adventitious root emergence; afterward, O₂ partial pressure changes were measured using a Clark-type O₂ microelectrode. O₂ concentrations in the adventitious roots decreased when N₂ was injected, regardless of the presence of light, indicating that the O₂ source was not photosynthetic when bark was removed. New adventitious roots developed near the surface when the water level increased, and O₂ conditions above the raised water level influenced O₂ concentrations in adventitious roots. O₂ concentrations in adventitious roots that developed before the water level increased were lower than in the newly developed adventitious roots but increased when the O₂ concentrations above the original water level increased. Our study highlights morphological changes, such as the development of adventitious roots, as environmental adaptation mechanisms. By revealing O₂ sources in S. kunstleri under hypoxic environments, we offer insights into the challenges of long-term adaptation to changing environments in woody plants.

Role of Epichloë Endophytes in Improving Host Grass Resistance Ability and Soil Properties

The past decade has witnessed significant advances in understanding the interaction between grasses and systemic fungal endophytes of the genus Epichloë, with evidence that plants have evolved multiple strategies to cope with abiotic stresses by reprogramming physiological responses. Soil nutrients directly affect plant growth, while soil microbes are also closely connected to plant growth and health. Epichloë endophytes could affect soil fertility by modifying soil nutrient contents and soil microbial diversity. Therefore, we analyze recent advances in our understanding of the role of Epichloë endophytes under the various abiotic stresses and the role of grass-Epichloë symbiosis on soil fertility. Various cool-season grasses are infected by Epichloë species, which contribute to health, growth, persistence, and seed survival of host grasses by regulating key systems, including photosynthesis, osmotic regulation, and antioxidants and activity of key enzymes of host physiology processes under abiotic stresses. The Epichloë endophyte offers significant prospects to magnify the crop yield, plant resistance, and food safety in ecological systems by modulating soil physiochemical properties and soil microbes. The enhancing resistance of host grasses to abiotic stresses by an Epichloë endophyte is a complex manifestation of different physiological and biochemical events through regulating soil properties and soil microbes by the fungal endophyte. The Epichloë-mediated mechanisms underlying regulation of abiotic stress responses are involved in osmotic adjustment, antioxidant machinery, photosynthetic system, and activity of key enzymes critical in developing plant adaptation strategies to abiotic stress. Therefore, the Epichloë endophytes are an attractive choice in increasing resistance of plants to abiotic stresses and are also a good candidate for improving soil fertility and regulating microbial diversity to improve plant growth.

The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings

The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogen invasion-but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here, we characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for several previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 min, and increased transcript levels of mechano-inducible genes within 60 min. We also show that cell swelling induces programmed cell death within 3 h in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.

Resistance of some commercial walnut cultivars and genotypes to Aceria tristriata (Nalepa) (Acari: Eriophyidae) and its correlation with some plant features

BACKGROUND

The walnut leaf gall mite (WLGM) (Aceria tristriata (Nalepa)) is one of the major pests of walnut in western Iran. The use of a resistant variety is an economical and environment-friendly method of pest control. The aim of the present study is to assess resistance of some walnut cultivars and genotypes in relation to WLGM. Also, the current research aimed to study a possible correlation between resistance with plant morphological and biochemical features.

RESULTS

Based on the leaf damage index (number of galls per leaf and plant, the percentage of infested leaves and the percentage of leaf injury area) induced by WLGM, the studied cultivars and genotypes were classified into four groups from susceptible to approximately resistant. Free-choice experiments indicated that Jamal and Chandler cultivars were colonized by lower densities of WLGM, whereas Seedling, Hartly, Lara and Z60 hosted denser populations. In antibiosis assay, the highest mite density was created in the galls on the leaves of Seedling and Hartly, whereas lowest mite density was observed in galled leaves of Chandler and Jamal cultivars.

CONCLUSION

Results from biochemical assays showed that nearly all evaluated biomarkers had negative correlation with number of galls per leaf and mite density. Generally, resistant cultivars (Chandler, Jamal and Pedro) significantly produced defensive compounds more than those of controls after mite infestation. Also, it is worth noting that, the content of photosynthetic pigments significantly reduced in susceptible cultivars after mite infestation. The obtained results from this study can be useful for provisional resistance screening. © 2019 Society of Chemical Industry.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Flood tolerance in two tree species that inhabit both the Amazonian floodplain and the dry Cerrado savanna of Brazil

Comparing plants of the same species thriving in flooded and non-flooded ecosystems helps to clarify the interplay between natural selection, phenotypic plasticity and stress adaptation. We focussed on responses of seeds and seedlings of Genipa americana and Guazuma ulmifolia to substrate waterlogging or total submergence. Both species are commonly found in floodplain forests of Central Amazonia and in seasonally dry savannas of Central Brazil (Cerrado). Although seeds of Amazonian and Cerrado G. americana were similar in size, the germination percentage of Cerrado seeds was decreased by submergence (3 cm water) and increased in Amazonian seeds. The seeds of Amazonian G. ulmifolia were heavier than Cerrado seeds, but germination of both types was unaffected by submergence. Three-month-old Amazonian and Cerrado seedlings of both species survived 30 days of waterlogging or submersion despite suffering significant inhibition in biomass especially if submerged. Shoot elongation was also arrested. Submersion triggered chlorosis and leaf abscission in Amazonian and Cerrado G. ulmifolia while waterlogging did so only in Cerrado seedlings. During 30 days of re-exposure to non-flooded conditions, G. ulmifolia plants that lost their leaves produced a replacement flush. However, they attained only half the plant dry mass of non-flooded plants. Both submerged and waterlogged G. americana retained their leaves. Consequently, plant dry mass after 30 days recovery was less depressed by these stresses than in G. ulmifolia. Small amounts of cortical aerenchyma were found in roots 2 cm from the tip of well-drained plants. The amount was increased by flooding. Waterlogging but not submergence promoted hypertrophy of lenticels at the stem base of both species and adventitious rooting in G. ulmifolia. Despite some loss of performance in dryland plants, flood tolerance traits were present in wetland and dryland populations of both species. They are part of an overall stress-response potential that permits flexible acclimation to locally flooded conditions.

Cell-Based Phenotyping Reveals QTL for Membrane Potential Maintenance Associated with Hypoxia and Salinity Stress Tolerance in Barley

Waterlogging and salinity are two major abiotic stresses that hamper crop production world-wide resulting in multibillion losses. Plant abiotic stress tolerance is conferred by many interrelated mechanisms. Amongst these, the cell's ability to maintain membrane potential (MP) is considered to be amongst the most crucial traits, a positive relationship between the ability of plants to maintain highly negative MP and its tolerance to both salinity and waterlogging stress. However, no attempts have been made to identify quantitative trait loci (QTL) conferring this trait. In this study, the microelectrode MIFE technique was used to measure the plasma membrane potential of epidermal root cells of 150 double haploid (DH) lines of barley (Hordeum vulgare L.) from a cross between a Chinese landrace TX9425 and Japanese malting cultivar Naso Nijo under hypoxic conditions. A major QTL for the MP in the epidermal root cells in hypoxia-exposed plants was identified. This QTL was located on 2H, at a similar position to the QTL for waterlogging and salinity tolerance reported in previous studies. Further analysis confirmed that MP showed a significant contribution to both waterlogging and salinity tolerance. The fact that the QTL for MP was controlled by a single major QTL illustrates the power of the single-cell phenotyping approach and opens prospects for fine mapping this QTL and thus being more effective in marker assisted selection.

Effect of waterlogging at different growth stages on some morphological traits of wheat varieties

Excess rainfalls may be the cause of waterlogging in soil, which affects the growth and development of wheat. Therefore, the objectives of this study were to examine the effects of waterlogging on shoot and root growth and physiological characteristics of wheat. Three experiments were conducted: experiment 1 (E1): evaluation of seedling growth on ten Iranian winter wheat varieties with waterlogging periods (1-4, 4-8, 8-12, and 12-16 days starting from seed germination). Seminal roots and plumule were investigated at seedling. The others are E2: pretreatment of waterlogging (15 days) at tillering and stem elongation stages and its effects on shoot and root growth at anthesis stage and experiment 3 (E3): pretreatment of waterlogging (15 days) at tillering and jointing stages and its effects on yield and yield components and also evaluation of stress tolerance indexes. The results of the seedling growth test (E1) showed that 1-4- and 4-8-day waterlogging severity reduced seminal root length (94.5 to 93.7 %) and plumule length (86.2 to 50.0 %) compared to control. Results of E2 indicated that waterlogging stress decreased shoot dry weight, root dry weight, total secondary root length, and chlorophyll a + b content of flag leaf by 28-31, 44-35, 20-31, and 28-35 %, respectively. Also, result of E3 showed that the grain yields of wheat varieties at two conditions of stress were different in base tolerance indexes. In general, the responses of wheat varieties to waterlogging were different at the three experiments. The varieties that had the most of dry weight and length of the root were tolerant. Thus, it is possible to use these characteristics as an index for selecting the varieties with tolerance to waterlogging.

Effects of Long-Term Periodic Submergence on Photosynthesis and Growth of Taxodium distichum and Taxodium ascendens Saplings in the Hydro-Fluctuation Zone of the Three Gorges Reservoir of China

Responses of bald cypress (Taxodium distichum) and pond cypress (Taxodium ascendens) saplings in photosynthesis and growth to long-term periodic submergence in situ in the hydro-fluctuation zone of the Three Gorges Dam Reservoir (TGDR) were studied. Water treatments of periodic deep submergence (DS) and moderate submergence (MS) in situ were imposed on 2-year-old bald cypress and pond cypress saplings. The effects of periodic submergence on photosynthesis and growth were investigated after 3 years (i.e. 3 cycles) compared to a control (i.e. shallow submergence, abbreviated as SS). Results showed that pond cypress had no significant change in net photosynthetic rate (Pn) in response to periodic moderate and deep submergence in contrast to a significant decrease in Pn of bald cypress under both submergence treatments, when compared to that of SS. Ratios of Chlorophyll a/b and Chlorophylls/Carotenoid of pond cypress were significantly increased in periodic moderate submergence and deep submergence, while bald cypress showed no significant change. Diameter at breast height (DBH) and tree height of both species were significantly reduced along with submergence depth. Relative diameter and height growth rates of the two species were also reduced under deeper submergence. Moreover, bald cypress displayed higher relative diameter growth rate than pond cypress under deep submergence mainly attributed to higher productivity of the larger crown area of bald cypress. When subjected to deep subergence, both species showed significant reduction in primary branch number, while in moderate submergence, bald cypress but not pond cypress showed significant reduction in primary branch number. These results indicate that both bald cypress and pond cypress are suitbale candidates for reforestation in the TGDR region thanks to their submergence tolerance characteristics, but bald cypress can grow better than pond cypress under deep submergence overall.

A Co-Opted Hormonal Cascade Activates Dormant Adventitious Root Primordia upon Flooding in Solanum dulcamara

Soil flooding is a common stress factor affecting plants. To sustain root function in the hypoxic environment, flooding-tolerant plants may form new, aerenchymatous adventitious roots (ARs), originating from preformed, dormant primordia on the stem. We investigated the signaling pathway behind AR primordium reactivation in the dicot species Solanum dulcamara Transcriptome analysis indicated that flooding imposes a state of quiescence on the stem tissue, while increasing cellular activity in the AR primordia. Flooding led to ethylene accumulation in the lower stem region and subsequently to a drop in abscisic acid (ABA) level in both stem and AR primordia tissue. Whereas ABA treatment prevented activation of AR primordia by flooding, inhibition of ABA synthesis was sufficient to activate them in absence of flooding. Together, this reveals that there is a highly tissue-specific response to reduced ABA levels. The central role for ABA in the response differentiates the pathway identified here from the AR emergence pathway known from rice (Oryza sativa). Flooding and ethylene treatment also induced expression of the polar auxin transporter PIN2, and silencing of this gene or chemical inhibition of auxin transport inhibited primordium activation, even though ABA levels were reduced. Auxin treatment, however, was not sufficient for AR emergence, indicating that the auxin pathway acts in parallel with the requirement for ABA reduction. In conclusion, adaptation of S. dulcamara to wet habitats involved co-option of a hormonal signaling cascade well known to regulate shoot growth responses, to direct a root developmental program upon soil flooding.

Introduction to the Special Issue: Electrons, water and rice fields: plant response and adaptation to flooding and submergence stress

Flooding and submergence impose widespread and unpredictable environmental stresses on plants and depress the yield of most food crops. The problem is increasing, as is the need for greater food production from an expanding human population. The incompatibility of these opposing trends creates an urgent need to improve crop resilience to flooding in its multifarious forms. This Special Issue brings together research findings from diverse plant species to address the challenge of enhancing adaptation to flooding in major crops and learning from tactics of wetland plants. Here we provide an overview of the articles, with attempts to summarize how recent research results are being used to produce varieties of crop plants with greater flooding tolerance, notably in rice. The progress is considerable and based firmly on molecular and physiological research findings. The article also sets out how next-generation improvements in crop tolerance are likely to be achieved and highlights some of the new research that is guiding the development of improved varieties. The potential for non-model species from the indigenous riparian flora to uncover and explain novel adaptive mechanisms of flooding tolerance that may be introduced into crop species is also explored. The article begins by considering how, despite the essential role of water in sustaining plant life, floodwater can threaten its existence unless appropriate adaptations are present. Central to resolving the contradiction is the distinction between the essential role of cellular water as the source of electrons and protons used to build and operate the plant after combining with CO2 and O2 and the damaging role of extracellular water that, in excess, interferes with the union of these gases with photosynthetic or respiratory electrons and protons.

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats

Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusii respectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous (dN/dS) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of R. bungei potentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating 'water transport process' and 'microtubule cytoskeleton organization'. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats.

Physiological integration enhanced the tolerance of Cynodon dactylon to flooding

Many flooding-tolerant species are clonal plants; however, the effects of physiological integration on plant responses to flooding have received limited attention. We hypothesise that flooding can trigger changes in metabolism of carbohydrates and ROS (reactive oxygen species) in clonal plants, and that physiological integration can ameliorate the adverse effects of stress, subsequently restoring the growth of flooded ramets. In the present study, we conducted a factorial experiment combining flooding to apical ramets and stolon severing (preventing physiological integration) between apical and basal ramets of Cynodon dactylon, which is a stoloniferous perennial grass with considerable flooding tolerance. Flooding-induced responses including decreased root biomass, accumulation of soluble sugar and starch, as well as increased activity of superoxide dismutase (SOD) and ascorbate peroxidase (APX) in apical ramets. Physiological integration relieved growth inhibition, carbohydrate accumulation and induction of antioxidant enzyme activity in stressed ramets, as expected, without any observable cost in unstressed ramets. We speculate that relief of flooding stress in clonal plants may rely on oxidising power and electron acceptors transferred between ramets through physiological integration.

Drowned, buried and carried away: effects of plant traits on the distribution of native and alien species in riparian ecosystems

Riparian vegetation is exposed to stress from inundation and hydraulic disturbance, and is often rich in native and alien plant species. We describe 35 traits that enable plants to cope with riparian conditions. These include traits for tolerating or avoiding anoxia and enabling underwater photosynthesis, traits that confer resistance and resilience to hydraulic disturbance, and attributes that facilitate dispersal, such as floating propagules. This diversity of life-history strategies illustrates that there are many ways of sustaining life in riparian zones, which helps to explain high riparian biodiversity. Using community assembly theory, we examine how adaptations to inundation, disturbance and dispersal shape plant community composition along key environmental gradients, and how human actions have modified communities. Dispersal-related processes seem to explain many patterns, highlighting the influence of regional processes on local species assemblages. Using alien plant invasions like an (uncontrolled) experiment in community assembly, we use an Australian and a global dataset to examine possible causes of high degrees of riparian invasion. We found that high proportions of alien species in the regional species pools have invaded riparian zones, despite not being riparian specialists, and that riparian invaders disperse in more ways, including by water and humans, than species invading other ecosystems.

Biotechnological approaches to creation of hypoxia and anoxia tolerant plants

The present work provides results of a number of biotechnological studies aimed at creating cell lines and entire plants resistant to anaerobic stress. Developed biotechnological approaches were based on earlier fundamental researches into anaerobic stress in plants, so "Introduction" briefly covers the importance of the problem and focuses on works considering two main strategies of plants adaptation to anaerobic stress. Those are adaptation at molecular level where key factor is anaerobic metabolism of energy (true tolerance) and adaptation of the entire plant via formation of aerenchyma and facilitated transportation of oxygen (apparent tolerance). Thus, sugarcane and wheat cells resistant to anaerobic stress were obtained through consecutive in vitro selection under conditions of anoxia and absence of exogenous carbohydrates. Tolerant wheat cells were used to regenerate entire plants of higher resistance to root anaerobiosis. It has been demonstrated that cells tolerance to anoxia is significantly supported by their ability to utilize exogenous nitrate. Cells tolerance established itself at the genetic level and was inherited by further generations. Apart from that, other successful attempts to increase tolerance of plants to anaerobic stress by means of stimulation of glycolysis and overexpression of genes responsible for cytokinin synthesis and programmed cell death are also discussed. The presented data proved the notion of two main strategies of plants adaptation to anaerobic stress proposed earlier on the base of fundamental studies.

Changes in carbohydrate content and membrane stability of two ecotypes of Calamagrostis arundinacea growing at different elevations in the drawdown zone of the Three Gorges Reservoir

Background

The Three Gorges project has caused many ecosystem problems. Ecological restoration using readily-available plants is an effective way of mitigating environmental impacts. Two perennial submergence-tolerant ecotypes of Calamagrostis arundinacea were planted in an experimental field in the drawdown zone. Responses of the two plant ecotypes to flooding stress in the drawdown zone were unknown.

Methodology/Principal Findings

Carbohydrate content and membrane stability, two key factors for survival of plants under flooding stress, of two ecotypes (designated “dwarf” and “green”) of C. arundinacea growing at different elevations of the drawdown zone were investigated. Live stems (LS) and dead stems (DS) of the two plant ecotypes at eight elevations (175, 170, 162, 160, 158, 155, 152 m and 149 m) were sampled. Contents of soluble sugar, starch and malondialdehyde (MDA), as well as plasma membrane permeability of live stems were measured. The lowest elevations for survival of dwarf and green C. arundinacea were 160 m and 158 m, respectively. Soluble sugar content of live stems of both ecotypes decreased with elevation, with amounts from an elevation of 170 m being lower than from an elevation of 175 m. MDA content and plasma membrane permeability in live stems of green C. arundinacea did not increase with the decrease in elevation, while these measures in dwarf C. arundinacea from an elevation of 162 m were significantly higher than from an elevation of 175 m.

Conclusions

Carbohydrate content, especially soluble sugar content, in both ecotypes was more sensitive to flooding stress than membrane stability. Green C. arundinacea had a higher tolerance to submergence than dwarf C. arundinacea, and thus green C. arundinacea can be planted at lower elevations than dwarf C. arundinacea.

Anatomical aspects of angiosperm root evolution

BACKGROUND AND AIMS

Anatomy had been one of the foundations in our understanding of plant evolutionary trends and, although recent evo-devo concepts are mostly based on molecular genetics, classical structural information remains useful as ever. Of the various plant organs, the roots have been the least studied, primarily because of the difficulty in obtaining materials, particularly from large woody species. Therefore, this review aims to provide an overview of the information that has accumulated on the anatomy of angiosperm roots and to present possible evolutionary trends between representatives of the major angiosperm clades.

SCOPE

This review covers an overview of the various aspects of the evolutionary origin of the root. The results and discussion focus on angiosperm root anatomy and evolution covering representatives from basal angiosperms, magnoliids, monocots and eudicots. We use information from the literature as well as new data from our own research.

KEY FINDINGS

The organization of the root apical meristem (RAM) of Nymphaeales allows for the ground meristem and protoderm to be derived from the same group of initials, similar to those of the monocots, whereas in Amborellales, magnoliids and eudicots, it is their protoderm and lateral rootcap which are derived from the same group of initials. Most members of Nymphaeales are similar to monocots in having ephemeral primary roots and so adventitious roots predominate, whereas Amborellales, Austrobaileyales, magnoliids and eudicots are generally characterized by having primary roots that give rise to a taproot system. Nymphaeales and monocots often have polyarch (heptarch or more) steles, whereas the rest of the basal angiosperms, magnoliids and eudicots usually have diarch to hexarch steles.

CONCLUSIONS

Angiosperms exhibit highly varied structural patterns in RAM organization; cortex, epidermis and rootcap origins; and stele patterns. Generally, however, Amborellales, magnoliids and, possibly, Austrobaileyales are more similar to eudicots, and the Nymphaeales are strongly structurally associated with the monocots, especially the Acorales.

Novel Prunus rootstock somaclonal variants with divergent ability to tolerate waterlogging

Plants require access to free water for nutrient uptake, but excess water surrounding the roots can be injurious or even lethal because it blocks the transfer of free oxygen between the soil and the atmosphere. Genetic improvement efforts in this study were focused on the increased tolerance in roots to waterlogging. Among a pool of clones generated in vitro from leaf explants of rootstock Mr.S.2/5 of Prunus cerasifera L., the S.4 clone was flood tolerant whereas the S.1 clone was sensitive. The S.4 clone formed adventitious roots on exposure to flooding. Moreover, the chlorophyll content and mitochondrial activity in the leaf and root, soluble sugar content, alcohol dehydrogenase activity and ethylene content were different between the clones. The sorbitol transporter gene (SOT1) was up-regulated during hypoxia, the alcohol dehydrogenase genes (ADH1 and ADH3) were up-regulated in the leaves and down-regulated in the roots of the S.4 clone during hypoxia, and the 1-aminocyclopropane-1-oxidase gene (ACO1) was up-regulated in the leaves and roots of the S.4 clone during hypoxia and down-regulated in the wild-type roots. In addition, in the S.4 root, hypoxia induced significant down-regulation of a glycosyltransferase-like gene (GTL), which has a yet-undefined role. Although the relevant variation in the S.4 genome has yet to be determined, genetic alteration clearly conferred a flooding-tolerant phenotype. The isolation of novel somaclonals with the same genomic background but with divergent tolerance to flooding may offer new insights in the elucidation of the genetic machinery of resistance to flooding and aid in the selection of new Prunus rootstocks to be used in various adverse environments.

Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding

A proteomic approach was used to identify proteins involved in post-flooding recovery in soybean roots. Two-day-old soybean seedlings were flooded with water for up to 3 days. After the flooding treatment, seedlings were grown until 7 days after sowing and root proteins were then extracted and separated using two-dimensional polyacrylamide gel electrophoresis (2-DE). Comparative analysis of 2-D gels of control and 3 day flooding-experienced soybean root samples revealed 70 differentially expressed protein spots, from which 80 proteins were identified. Many of the differentially expressed proteins are involved in protein destination/storage and metabolic processes. Clustering analysis based on the expression profiles of the 70 differentially expressed protein spots revealed that 3 days of flooding causes significant changes in protein expression, even during post-flooding recovery. Three days of flooding resulted in downregulation of ion transport-related proteins and upregulation of proteins involved in cytoskeletal reorganization, cell expansion, and programmed cell death. Furthermore, 7 proteins involved in cell wall modification and S-adenosylmethionine synthesis were identified in roots from seedlings recovering from 1 day of flooding. These results suggest that alteration of cell structure through changes in cell wall metabolism and cytoskeletal organization may be involved in post-flooding recovery processes in soybean seedlings.

Endogenous abscisic acid as a key switch for natural variation in flooding-induced shoot elongation

Elongation of leaves and stem is a key trait for survival of terrestrial plants during shallow but prolonged floods that completely submerge the shoot. However, natural floods at different locations vary strongly in duration and depth, and, therefore, populations from these locations are subjected to different selection pressure, leading to intraspecific variation. Here, we identified the signal transduction component that causes response variation in shoot elongation among two accessions of the wetland plant Rumex palustris. These accessions differed 2-fold in petiole elongation rates upon submergence, with fast elongation found in a population from a river floodplain and slow elongation in plants from a lake bank. Fast petiole elongation under water consumes carbohydrates and depends on the (inter)action of the plant hormones ethylene, abscisic acid, and gibberellic acid. We found that carbohydrate levels and dynamics in shoots did not differ between the fast and slow elongating plants, but that the level of ethylene-regulated abscisic acid in petioles, and hence gibberellic acid responsiveness of these petioles explained the difference in shoot elongation upon submergence. Since this is the exact signal transduction level that also explains the variation in flooding-induced shoot elongation among plant species (namely, R. palustris and Rumex acetosa), we suggest that natural selection results in similar modification of regulatory pathways within and between species.

Flooding induced emissions of volatile signalling compounds in three tree species with differing waterlogging tolerance

To gain insight into variations in waterlogging responsiveness, net assimilation rate, stomatal conductance, emissions of isoprene and marker compounds of anoxic metabolism ethanol and acetaldehyde, and stress marker compounds nitric oxide (NO), volatile products of lipoxygenase (LOX) pathway and methanol were studied in seedlings of temperate deciduous tree species Alnus glutinosa, Populus tremula and Quercus rubra (from highest to lowest waterlogging tolerance) throughout sustained root zone waterlogging of up to three weeks. In all species, waterlogging initially resulted in reductions in net assimilation and stomatal conductance and enhanced emissions of ethanol, acetaldehyde, NO, LOX products and methanol, followed by full or partial recovery depending on process and species. Strong negative correlations between g(s) and internal NO concentration and NO flux, valid within and across species, were observed throughout the experiment. Isoprene emission capacity was not related to waterlogging tolerance. Less waterlogging tolerant species had greater reduction and smaller acclimation capacity in foliage physiological potentials, and larger emission bursts of volatile stress marker compounds. These data collectively provide encouraging evidence that emissions of volatile organics and NO can be used as quantitative measures of stress tolerance and acclimation kinetics in temperate trees.

Stem hypertrophic lenticels and secondary aerenchyma enable oxygen transport to roots of soybean in flooded soil

BACKGROUND AND AIMS

Aerenchyma provides a low-resistance O(2) transport pathway that enhances plant survival during soil flooding. When in flooded soil, soybean produces aerenchyma and hypertrophic stem lenticels. The aims of this study were to investigate O(2) dynamics in stem aerenchyma and evaluate O(2) supply via stem lenticels to the roots of soybean during soil flooding.

METHODS

Oxygen dynamics in aerenchymatous stems were investigated using Clark-type O(2) microelectrodes, and O(2) transport to roots was evaluated using stable-isotope (18)O(2) as a tracer, for plants with shoots in air and roots in flooded sand or soil. Short-term experiments also assessed venting of CO(2) via the stem lenticels.

KEY RESULTS

The radial distribution of the O(2) partial pressure (pO(2)) was stable at 17 kPa in the stem aerenchyma 15 mm below the water level, but rapidly declined to 8 kPa at 200-300 microm inside the stele. Complete submergence of the hypertrophic lenticels at the stem base, with the remainder of the shoot still in air, resulted in gradual declines in pO(2) in stem aerenchyma from 17.5 to 7.6 kPa at 13 mm below the water level, and from 14.7 to 6.1 kPa at 51 mm below the water level. Subsequently, re-exposure of the lenticels to air caused pO(2) to increase again to 14-17 kPa at both positions within 10 min. After introducing (18)O(2) gas via the stem lenticels, significant (18)O(2) enrichment in water extracted from roots after 3 h was confirmed, suggesting that transported O(2) sustained root respiration. In contrast, slight (18)O(2) enrichment was detected 3 h after treatment of stems that lacked aerenchyma and lenticels. Moreover, aerenchyma accelerated venting of CO(2) from submerged tissues to the atmosphere.

CONCLUSIONS

Hypertrophic lenticels on the stem of soybean, just above the water surface, are entry points for O(2), and these connect to aerenchyma and enable O(2) transport into roots in flooded soil. Stems that develop aerenchyma thus serve as a 'snorkel' that enables O(2) movement from air to the submerged roots.

Flooding tolerance: suites of plant traits in variable environments

Flooding regimes of different depths and durations impose selection pressures for various traits in terrestrial wetland plants. Suites of adaptive traits for different flooding stresses, such as soil waterlogging (short or long duration) and full submergence (short or long duration - shallow or deep), are reviewed. Synergies occur amongst traits for improved internal aeration, and those for anoxia tolerance and recovery, both for roots during soil waterlogging and shoots during submergence. Submergence tolerance of terrestrial species has recently been classified as either the Low Oxygen Quiescence Syndrome (LOQS) or the Low Oxygen Escape Syndrome (LOES), with advantages, respectively, in short duration or long duration (shallow) flood-prone environments. A major feature of species with the LOQS is that shoots do not elongate upon submergence, whereas those with the LOES show rapid shoot extension. In addition, plants faced with long duration deep submergence can demonstrate aspects of both syndromes; shoots do not elongate, but these are not quiescent, as new aquatic-type leaves are formed. Enhanced entries of O₂ and CO₂ from floodwaters into acclimated leaves, minimises O₂ deprivation and improves underwater photosynthesis, respectively. Evolution of 'suites of traits' are evident in wild wetland species and in rice, adapted to particular flooding regimes.