How plants cope with complete submergence

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

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

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

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

Sub1 QTL confers submergence tolerance in rice through nitro-oxidative regulation and phytohormonal signaling

Constant change in global climate has become the most important limiting factor to crop productivity. Asymmetrical precipitations are causing recurrent flood events around the world. Submergence is one of the most detrimental abiotic stresses for sustainable rice production in the rainfed ecosystems of Southeast Asia. Therefore, the development of submergence-tolerant rice is an essential requirement to encounter food security. Submergence tolerance in rice is governed by the major quantitative trait locus (QTL) designated as Submergence1 (Sub1) near the centromere of chromosome 9. The introduction of the Sub1 in high-yielding rice varieties producing near-isogenic lines (NILs) has shown extreme submergence tolerance. The present study aimed to understand the responses of rice genotype IR64 and its Sub1 NIL IR64 Sub1 following one week of complete submergence treatment. Submergence imposed severe nitro-oxidative stress in both the rice genotypes, consequently disrupting the cellular redox homeostasis. In this study, IR64 exhibited higher NADPH oxidase activity accompanied by increased reactive oxygen species, reactive nitrogen species, and malondialdehyde buildups and cell death under submergence. Higher accumulations of 1-Aminocyclopropane-1-carboxylic acid, gibberellic acid, and Indole-3-acetic acid were also observed in IR64 which accelerated the plant growth and root cortical aerenchyma development following submergence. In contrast, IR64 Sub1 had enhanced submergence tolerance associated with an improved antioxidant defense system with sustainable morpho-physiological activities and restricted root aerenchyma formation. The comprehensive analyses of the responses of rice genotypes with contrasting submergence tolerance may demonstrate the intricacies of rice under complete submergence and may potentially contribute to improving stress resilience by advancing our understanding of the mechanisms of submergence tolerance in rice.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Comparison of Growth and Physiological Effects of Soil Moisture Regime on Plantago maritima Plants from Geographically Isolated Sites on the Eastern Coast of the Baltic Sea

The aim of the present study was to evaluate the morphological and physiological responses of P. maritima plants from five geographically isolated sites growing in habitats with different conditions to different substrate moisture levels in controlled conditions. Plants were produced from seed and cultivated in a greenhouse at four relatively constant soil moisture regimes: at 25, 50, and 75% soil water content and in soil flooded 3 cm above the surface (80% F). The two morphological traits that varied most strikingly among P. maritima accessions were the number of flower stalks and the number of leaves. Only plants from two accessions uniformly produced generative structures, and allocation to flowering was suppressed by both low moisture and flooding. Optimum shoot biomass accumulation for all accessions was at 50 and 75% soil moisture. The Performance Index Total was the most sensitive among the measured photosynthesis-related parameters, and it tended to decrease with an increase in soil water content for all P. maritima accessions. The initial hypothesis-that plants from relatively dry habitats will have a higher tolerance against low soil water levels, but plants from relatively wet habitats will have a higher tolerance against waterlogged or flooded soil-was not proven. The existence of three ecotypes of P. maritima within the five accessions from geographically isolated subpopulations on the eastern coast of the Baltic Sea at the level of morphological responses to soil water content can be proposed. P. maritima plants can be characterized as extremely tolerant to soil waterlogging and highly tolerant to soil flooding and low soil water content.

Deciphering Physio-Biochemical Basis of Tolerance Mechanism for Sesame (Sesamum indicum L.) Genotypes under Waterlogging Stress at Early Vegetative Stage

Waterlogging represents a substantial agricultural concern, inducing harmful impacts on crop development and productivity. In the present study, 142 diverse sesame genotypes were examined during the early vegetative phase to assess their response under waterlogging conditions. Based on the severity of symptoms observed, 2 genotypes were classified as highly tolerant, 66 as moderately tolerant, 69 as susceptible, and 5 as highly susceptible. Subsequent investigation focused on four genotypes, i.e., two highly tolerant (JLT-8 and GP-70) and two highly susceptible (R-III-F6 and EC-335003). These genotypes were subjected to incremental stress periods (0 h, 24 h, 48 h, 72 h, and 96 h) to elucidate the biochemical basis of tolerance mechanisms. Each experiment was conducted as a randomized split-plot design with three replications, and the statistical significance of the treatment differences was determined using the one-way analysis of variance (ANOVA) followed by the Fisher least significant difference (LSD) test at p ≤ 0.05. The influence of waterlogging stress on morphological growth was detrimental for both tolerant and susceptible genotypes, with more severe consequences observed in the latter. Although adventitious roots were observed in both sets of genotypes above flooding levels, the tolerant genotypes exhibited a more rapid and vigorous development of these roots after 48 h of stress exposure. Tolerant genotypes displayed higher tolerance coefficients compared to susceptible genotypes. Furthermore, tolerant genotypes maintained elevated antioxidant potential, thereby minimizing oxidative stress. Conversely, susceptible genotypes exhibited higher accumulation of hydrogen peroxide (H2O2) and malondialdehyde content. Photosynthetic efficiency was reduced in all genotypes after 24 h of stress treatment, with a particularly drastic reduction in susceptible genotypes compared to their tolerant counterparts. Tolerant genotypes exhibited significantly higher activities of anaerobic metabolism enzymes, enabling prolonged survival under waterlogging conditions. Increase in proline content was observed in all the genotypes indicating the cellular osmotic balance adjustments in response to stress exposure. Consequently, the robust antioxidant potential and efficient anaerobic metabolism observed in the tolerant genotypes served as key mechanisms enabling their resilience to short-term waterlogging exposure. These findings underscore the promising potential of specific sesame genotypes in enhancing crop resilience against waterlogging stress, offering valuable insights for agricultural practices and breeding programs.

Ethylene signaling modulates air humidity responses in plants

Air humidity significantly impacts plant physiology. However, the upstream elements that mediate humidity sensing and adaptive responses in plants remain largely unexplored. In this study, we define high humidity-induced cellular features of Arabidopsis plants and take a quantitative phosphoproteomics approach to obtain a high humidity-responsive landscape of membrane proteins, which we reason are likely the early checkpoints of humidity signaling. We found that a brief high humidity exposure (i.e., 0.5 h) is sufficient to trigger extensive changes in membrane protein abundance and phosphorylation. Enrichment analysis of differentially regulated proteins reveals high humidity-sensitive processes such as 'transmembrane transport', 'response to abscisic acid', and 'stomatal movement'. We further performed a targeted screen of mutants, in which high humidity-responsive pathways/proteins are disabled, to uncover genes mediating high humidity sensitivity. Interestingly, ethylene pathway mutants (i.e., ein2 and ein3eil1) display a range of altered responses, including hyponasty, reactive oxygen species level, and responsive gene expression, to high humidity. Furthermore, we observed a rapid induction of ethylene biosynthesis genes and ethylene evolution after high humidity treatment. Our study sheds light on the potential early signaling events in humidity perception, a fundamental but understudied question in plant biology, and reveals ethylene as a key modulator of high humidity responses in plants.

Identification and characterization of waterlogging-responsive genes in the parental line of maize hybrid An'nong 876

Waterlogging stress is an important abiotic stress that adversely affects maize growth and yield. The mechanism regulating the early stage of the maize response to waterlogging stress is largely unknown. In this study, CM37 and cmh15 seedlings were treated with waterlogging stress and then examined in terms of their physiological changes. The results indicated that inbred line cmh15 is more tolerant to waterlogging stress and less susceptible to peroxide-based damages than CM37. The RNA sequencing analysis identified 1,359 down-regulated genes and 830 up-regulated genes in the waterlogging-treated cmh15 plants (relative to the corresponding control levels). According to the Gene Ontology analysis for the differentially expressed genes (DEGs), some important terms were identified which may play important roles in the response to waterlogging stress. Moreover, enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified for the DEGs. Furthermore, the substantial changes in the expression of 36 key transcription factors may be closely related to the maize in response to waterlogging stress. This study offers important insights into the mechanism in regulating maize tolerance to waterlogging stress, with important foundations for future research.

Shaking off the blow: plant adjustments during submergence and post-stress growth in Lotus forage species

Flooding significantly hampers global forage production. In flood-prone regions, Lotus tenuis and Lotus corniculatus are common forage legumes, yet little is known about their responses to partial or complete submergence. To address this, we evaluated 10 Lotus accessions subjected to 11days of either partial or complete submergence, analysing growth traits related to tolerance and recovery after de-submergence. Principal component analyses revealed that submergence associated growth parameters were linked to L. corniculatus accessions, whereas recovery was associated with L. tenuis accessions. Notably, in L. tenuis , recovery from complete submergence positively correlated with leaf mass fraction but negatively with root mass fraction, showing an opposite pattern than in L. corniculatus . Encouragingly, no trade-off was found between inherent growth capacity and submergence tolerance (both partial and complete) or recovery ability, suggesting genetic selection for increased tolerance would not compromise growth potential. L. tenuis exhibited accessions with both partial and complete submergence tolerance, making them versatile for flood-prone environments, whereas L. corniculatus accessions were better suited for partial submergence. These findings offer valuable insights to enhance forage production in flood-prone areas and guide the selection of appropriate Lotus accessions for specific flood conditions.

Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges

Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.

Niche construction and the environmental term of the price equation: How natural selection changes when organisms alter their environments

Organisms construct their own environments and phenotypes through the adaptive processes of habitat choice, habitat construction, and phenotypic plasticity. We examine how these processes affect the dynamics of mean fitness change through the environmental change term of the Price Equation. This tends to be ignored in evolutionary theory, owing to the emphasis on the first term describing the effect of natural selection on mean fitness (the additive genetic variance for fitness of Fisher's Fundamental Theorem). Using population genetic models and the Price Equation, we show how adaptive niche constructing traits favorably alter the distribution of environments that organisms encounter and thereby increase population mean fitness. Because niche-constructing traits increase the frequency of higher-fitness environments, selection favors their evolution. Furthermore, their alteration of the actual or experienced environmental distribution creates selective feedback between niche constructing traits and other traits, especially those with genotype-by-environment interaction for fitness. By altering the distribution of experienced environments, niche constructing traits can increase the additive genetic variance for such traits. This effect accelerates the process of overall adaption to the niche-constructed environmental distribution and can contribute to the rapid refinement of alternative phenotypic adaptations to different environments. Our findings suggest that evolutionary biologists revisit and reevaluate the environmental term of the Price Equation: owing to adaptive niche construction, it contributes directly to positive change in mean fitness; its magnitude can be comparable to that of natural selection; and, when there is fitness G × E, it increases the additive genetic variance for fitness, the much-celebrated first term.

Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.)

BACKGROUND

Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein family is plant-specific and has not been described previously. A basic analysis and expression profiling was performed, and the co-expression and interaction networks were constructed to explore the functions of DUF568 family in rice.

RESULTS

The phylogenetic tree showed that the 8, 9 and 11 DUF568 family members from rice, Arabidopsis and maize were divided into three groups. The evolutionary relationship between DUF568 members in rice and maize was close, while the genes in Arabidopsis were more distantly related. The cis-elements prediction showed that over 82% of the elements upstream of OsDUF568 genes were responsive to light and phytohormones. Gene expression profile prediction and RT-qPCR experiments revealed that OsDUF568 genes were highly expressed in leaves, stems and roots of rice seedling. The expression of some OsDUF568 genes varied in response to plant hormones (abscisic acid, 6-benzylaminopurine) and abiotic stress (drought and chilling). Further analysis of the co-expression and protein-protein interaction networks using gene ontology showed that OsDUF568 - related genes were enriched in cellular transports, metabolism and processes.

CONCLUSIONS

In summary, our findings suggest that the OsDUF568 family may be a vital gene family for the development of rice roots, leaves and stems. In addition, the OsDUF568 family may participate in abscisic acid and cytokinin signaling pathways, and may be related to abiotic stress resistance in these vegetative tissues of rice.

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.

A meta-analysis of plant tissue O2 dynamics

Adequate tissue O2 supply is crucial for plant function. We aimed to identify the environmental conditions and plant characteristics that affect plant tissue O2 status. We extracted data and performed meta-analysis on >1500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in roots to >53kPa in submerged, photosynthesising shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light×submergence' interaction as significant drivers of tissue O2 status. Median O2 status were especially low (Solanum tuberosum ) tubers and root nodules. Mean shoot and root O2 were ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2 , with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although use of miniaturised Clark-type O2 electrodes has enhanced understanding of plant O2 dynamics, application of non-invasive methods in plants is still lacking behind its widespread use in mammalian tissues.

Changes in terpene biosynthesis and submergence tolerance in cotton

BACKGROUND

Flooding is among the most severe abiotic stresses in plant growth and development. The mechanism of submergence tolerance of cotton in response to submergence stress is unknown.

RESULTS

The transcriptome results showed that a total of 6,893 differentially expressed genes (DEGs) were discovered under submergence stress. Gene Ontology (GO) enrichment analysis showed that DEGs were involved in various stress or stimulus responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs related to plant hormone signal transduction, starch and sucrose metabolism, glycolysis and the biosynthesis of secondary metabolites were regulated by submergence stress. Eight DEGs related to ethylene signaling and 3 ethylene synthesis genes were identified in the hormone signal transduction. For respiratory metabolism, alcohol dehydrogenase (ADH, GH_A02G0728) and pyruvate decarboxylase (PDC, GH_D09G1778) were significantly upregulated but 6-phosphofructokinase (PFK, GH_D05G0280), phosphoglycerate kinase (PGK, GH_A01G0945 and GH_D01G0967) and sucrose synthase genes (SUS, GH_A06G0873 and GH_D06G0851) were significantly downregulated in the submergence treatment. Terpene biosynthetic pathway-related genes in the secondary metabolites were regulated in submergence stress.

CONCLUSIONS

Regulation of terpene biosynthesis by respiratory metabolism may play a role in enhancing the tolerance of cotton to submergence under flooding. Our findings showed that the mevalonate pathway, which occurs in the cytoplasm of the terpenoid backbone biosynthesis pathway (ko00900), may be the main response to submergence stress.

Modeling strategies and data needs for representing coastal wetland vegetation in land surface models

Vegetated coastal ecosystems sequester carbon rapidly relative to terrestrial ecosystems. Coastal wetlands are poorly represented in land surface models, but work is underway to improve process-based, predictive modeling of these ecosystems. Here, we identify guiding questions, potential simulations, and data needs to make progress in improving representation of vegetation in terrestrial-aquatic interfaces, with a focus on coastal and estuarine ecosystems. We synthesize relevant plant traits and environmental controls on vegetation that influence carbon cycling in coastal ecosystems. We propose that models include separate plant functional types (PFTs) for mangroves, graminoid salt marshes, and succulent salt marshes to adequately represent the variation in aboveground and belowground productivity between common coastal wetland vegetation types. We also discuss the drivers and carbon storage consequences of shifts in dominant PFTs. We suggest several potential approaches to represent the diversity in vegetation tolerance and adaptations to fluctuations in salinity and water level, which drive key gradients in coastal wetland ecosystems. Finally, we discuss data needs for parameterizing and evaluating model implementations of coastal wetland vegetation types and function.

Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress

BACKGROUND

Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination.

RESULTS

The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein).

CONCLUSION

A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.

In situ mapping of ion distribution profiles and gene expression reveals interactions between hypoxia and Mn2+/Fe2+ availability in barley roots

Flooding stress affects soil properties thus altering the availability, uptake, and transport of mineral nutrients in plant roots. Flooding stress also increases the amount of soluble Mn²⁺ and Fe²⁺ in the soil and their uptake by plants, causing elemental toxicity. However, as oxygen profiles in plant roots are not uniform, it is still unclear how soil flooding will affect Mn²⁺/Fe²⁺ absorption and distribution in different cell types and tissues. In this study, waterlogging sensitive barley variety NasoNijo (NN) and tolerant variety TX9425 (TX) were exposed to hypoxia, metal (Mn²⁺ and Fe²⁺), and combined hypoxia + metal treatment to map the in situ ion profiles at different regions of barley root. We found that combined hypoxia and metal stress causes significantly more reduction in plant biomass compared with the single submergence or metal stress. Despite this, more Fe and Mn were accumulated under metal stress condition than those under combined stress, regardless of variety. Cultivar NN absorbed more Fe and Mn than TX in the cortical cells of the root meristem and in the mature zone under metal stress which was also verified by histochemical detection. In the mature zone, the expressions of Fe and Mn transporter genes including HvADPRibase-Mn (Manganese-dependent ADP-ribose), HvZIP1 (zinc-regulated transporter /Fe-regulated transporter-like protein 1), HvYS1 (yellow stripe 1), HvNRAMP5 (Natural Resistance-Associated Macrophage Protein 5) were significantly downregulated under all three treatments in both barley varieties except HvADPRibase-Mn HvZIP1 cortex of TX were unchanged under metal stress. Interestingly, the transcripts of HvMTP1 (metal tolerance protein 1) were significantly downregulated by metal and combined stress in stele and upregulated by hypoxia and metal stress in cortex of TX, but not affected in NN. It is concluded that Fe and Mn absorption involving HvMTP1is associated with the extent of waterlogging tolerance in barley.

Physiology and proteomics analyses reveal the response mechanisms of Rhizophora mucronata seedlings to prolonged complete submergence

Mangrove seedlings are subject to natural tidal inundation, while occasional flooding may lead to complete submergence. Complete submergence reduces light availability and limits gas exchange, affecting several plant metabolic processes. The present study focuses on Rhizophora mucronata, a common mangrove species found along the coasts of Thailand and the Malay Peninsula. To reveal response mechanisms of R. mucronata seedlings to submergence, a physiological investigation coupled with proteomic analyses of leaf and root tissues was carried out in plants subjected to 20 days of control (drained) or submerged conditions. Submerged seedlings showed decreased photosynthetic activity, lower stomatal conductance, higher total antioxidant capacity in leaves and higher lipid peroxidation in roots than control plants. At the same time, tissue nutrient ion content displayed organ-specific responses. Proteome analysis revealed a significant change in 240 proteins in the leaves and 212 proteins in the roots. In leaves, most differentially accumulated proteins (DAPs) are associated with nucleic acids, stress response, protein transport, signal transduction, development and photosynthesis. In roots, most DAPs are associated with protein metabolic process, response to abiotic stimulus, nucleic acid metabolism and transport. Our study provides a comprehensive understanding of submergence responses in R. mucronata seedlings. The results suggest that submergence induced multifaceted stresses related to light limitation, oxidative stress and osmotic stress, but the responses are organ specific. The results revealed many candidate proteins which may be essential for survival of R. mucronata under prolonged submergence.

Multi-stress resilience in plants recovering from submergence

Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.

Rewiring of hormones and light response pathways underlies the inhibition of stomatal development in an amphibious plant Rorippa aquatica underwater

Land plants have evolved the ability to cope with submergence. Amphibious plants are adapted to both aerial and aquatic environments through phenotypic plasticity in leaf form and function, known as heterophylly. In general, underwater leaves of amphibious plants are devoid of stomata, yet their molecular regulatory mechanisms remain elusive. Using the emerging model of the Brassicaceae amphibious species Rorippa aquatica, we lay the foundation for the molecular physiological basis of the submergence-triggered inhibition of stomatal development. A series of temperature shift experiments showed that submergence-induced inhibition of stomatal development is largely uncoupled from morphological heterophylly and likely regulated by independent pathways. Submergence-responsive transcriptome analysis revealed rapid reprogramming of gene expression, exemplified by the suppression of RaSPEECHLESS and RaMUTE within 1 h and the involvement of light and hormones in the developmental switch from terrestrial to submerged leaves. Further physiological studies place ethylene as a central regulator of the submergence-triggered inhibition of stomatal development. Surprisingly, red and blue light have opposing functions in this process: blue light promotes, whereas red light inhibits stomatal development, through influencing the ethylene pathway. Finally, jasmonic acid counteracts the inhibition of stomatal development, which can be attenuated by the red light. The actions and interactions of light and hormone pathways in regulating stomatal development in R. aquatica are different from those in the terrestrial species, Arabidopsis thaliana. Thus, our work suggests that extensive rewiring events of red light to ethylene signaling might underlie the evolutionary adaption to water environment in Brassicaceae.

ADH Gene Cloning and Identification of Flooding-Responsive Genes in Taxodium distichum (L.) Rich

As a flooding-tolerant tree species, Taxodium distichum has been utilized in afforestation projects and proven to have important value in flooding areas. Alcohol dehydrogenase (ADH), which participates in ethanol fermentation, is essential for tolerance to the anaerobic conditions caused by flooding. In a comprehensive analysis of the ADH gene family in T. distichum, TdADHs were cloned on the basis of whole-genome sequencing, and then bioinformatic analysis, subcellular localization, and gene expression level analysis under flooding were conducted. The results show that the putative protein sequences of 15 cloned genes contained seven TdADHs and eight TdADH-like genes (one Class III ADH included) that were divided into five clades. All the sequences had an ADH_N domain, and except for TdADH-likeE2, all the other genes had an ADH_zinc_N domain. Moreover, the TdADHs in clades A, B, C, and D had a similar motif composition. Additionally, the number of TdADH amino acids ranged from 277 to 403, with an average of 370.13. Subcellular localization showed that, except for TdADH-likeD3, which was not expressed in the nucleus, the other genes were predominantly expressed in both the nucleus and cytosol. TdADH-likeC2 was significantly upregulated in all three organs (roots, stems, and leaves), and TdADHA3 was also highly upregulated under 24 h flooding treatment; the two genes might play key roles in ethanol fermentation and flooding tolerance. These findings offer a comprehensive understanding of TdADHs and could provide a foundation for the molecular breeding of T. distichum and current research on the molecular mechanisms driving flooding tolerance.

Abscisic acid modulates neighbor proximity-induced leaf hyponasty in Arabidopsis

Leaves of shade-avoiding plants such as Arabidopsis (Arabidopsis thaliana) change their growth pattern and position in response to low red to far-red ratios (LRFRs) encountered in dense plant communities. Under LRFR, transcription factors of the phytochrome-interacting factor (PIF) family are derepressed. PIFs induce auxin production, which is required for promoting leaf hyponasty, thereby favoring access to unfiltered sunlight. Abscisic acid (ABA) has also been implicated in the control of leaf hyponasty, with gene expression patterns suggesting that LRFR regulates the ABA response. Here, we show that LRFR leads to a rapid increase in ABA levels in leaves. Changes in ABA levels depend on PIFs, which regulate the expression of genes encoding isoforms of the enzyme catalyzing a rate-limiting step in ABA biosynthesis. Interestingly, ABA biosynthesis and signaling mutants have more erect leaves than wild-type Arabidopsis under white light but respond less to LRFR. Consistent with this, ABA application decreases leaf angle under white light; however, this response is inhibited under LRFR. Tissue-specific interference with ABA signaling indicates that an ABA response is required in different cell types for LRFR-induced hyponasty. Collectively, our data indicate that LRFR triggers rapid PIF-mediated ABA production. ABA plays a different role in controlling hyponasty under white light than under LRFR. Moreover, ABA exerts its activity in multiple cell types to control leaf position.

A simple and cost-effective method for studying anoxia tolerance in plants

Premise

We developed a novel, cost-effective protocol that facilitates testing anoxia tolerance in plants without access to specialized equipment.

Methods and Results

Arabidopsis thaliana and barley (Hordeum vulgare) seedlings were treated in airtight 2-L Kilner jars. An anoxic atmosphere was generated using Oxoid AnaeroGen 2.5-L sachets placed on in-house, custom-built wire stands. The performed experiments confirmed a higher sensitivity to low oxygen stress previously observed in anac017 A. thaliana mutants and the positive effect of exogenous sucrose on anoxia tolerance reported by previous studies in A. thaliana. Barley seedlings displayed typical responses to anoxia treatment, including shoot growth cessation and the induction of marker genes for anaerobic metabolism and ethylene biosynthesis in root tissue.

Conclusions

The results validate the novel method as an inexpensive, simple alternative for testing anoxia tolerance in plants, where access to an anaerobic workstation is not possible. The novel protocol requires minimum investment and is easily adaptable.

Hydropeaking impacts on riverine plants downstream from the world's largest hydropower dam, the Three Gorges Dam

Hydropeaking has become a global issue because of extensive hydropower dam construction worldwide. Yet, its ecological impacts on riverine ecosystems are not well studied. We explored the effects of hydropeaking on riverine plants, based on data from a ~300 km reach downstream of the world's largest hydropower dam, the Three Gorges Dam. We tested three hypotheses relating to hydropeaking impacts on species elevational distributions, assemblage structure and species-specific biomass patterns by generalized linear mixed modelling and joint species distribution modelling. We found that, first, hydropeaking greatly shaped species elevational ranges, leading to expansions of herbs to high elevations and shifting species dominance at low elevations. Secondly, we detected contrasting effects of hydropeaking on assemblage-level characteristics of herbs. The inundation induced by hydropeaking had strong effects on assemblage composition and biomass allocation, where more biomass was allocated to belowground part. Hydropeaking blurred the species richness-biomass relationship, although it had little effect on species richness or plot-level biomass. Thirdly, hydropeaking induced inundation was the most important covariate driving species biomass patterns of riverine plants, although complex species-specific effects were identified, and random effects were often large in fitted models. We concluded that hydropeaking likely acted as a major driver of plant community assembly in rivers with a hydropower dam. Conservation and restoration of riverine plants can benefit from the inclusion of water level management in operational schemes of hydropower dams, especially during the early life history stages.

Differences in the metabolic and functional mechanisms used to tolerate flooding in Guazuma ulmifolia (Lam.) from flood-prone Amazonian and dry Cerrado savanna populations

Flood tolerance is crucial to the survival of tree species subject to long periods of flooding, such as those present in the Amazonian várzea. Tolerance can be mediated by adjustments of metabolism, physiology and morphology, reinforcing the need to investigate the physiological and biochemical mechanisms used by tropical tree species to survive this stress. Moreover, such mechanisms may vary between populations that are subjected to differences in the frequency of flooding events. Here, we aimed to identify the mechanisms used by two populations of the tropical tree Guazuma ulmifolia (Lam.) to tolerate flooding: an Amazonian population frequently exposed to flooding and a Cerrado population, adapted to a dry environment. Young plants were subjected to a flooding of the roots and lower stem for 32 days, followed by 17 days of recovery. Amazonian plants exhibited greater increases in shoot length and higher maximum photosynthetic rate (Amax) compared with non-flooded plants from 7 days of flooding onwards, whereas increased Amax occurred later in flooded Cerrado plants and was not accompanied by increased shoot length. Lactate accumulated in roots of Cerrado plants after 24 h flooding, together with transcripts coding for lactate dehydrogenase in roots of both Cerrado and Amazonian plants. After 7 days of flooding, lactate decreased and alcohol dehydrogenase activity increased transiently, together with concentrations of alanine, γ-aminobutyric acid and succinate, indicating activation of metabolic processes associated with low oxygen availability. Other amino acids also increased in flooded Cerrado plants, revealing more extensive metabolic changes than in Amazonian plants. Wetland and dryland populations of G. ulmifolia revealed the great capacity to tolerate flooding stress through a suite of alterations in photosynthetic gas exchange and metabolism. However, the integrated physiological, biochemical and molecular analyses realized here indicated that wetland plants acclimatized more efficiently with increased shoot elongation and more rapid restoration of normal metabolism.

Leading trait dimensions in flood-tolerant plants

BACKGROUND AND AIMS

While trait-based approaches have provided critical insights into general plant functioning, we lack a comprehensive quantitative view on plant strategies in flooded conditions. Plants adapted to flooded conditions have specific traits (e.g. root porosity, low root/shoot ratio and shoot elongation) to cope with the environmental stressors including anoxic sediments, and the subsequent presence of phytotoxic compounds. In flooded habitats, plants also respond to potential nutrient and light limitations, e.g. through the expression of leaf economics traits and size-related traits, respectively. However, we do not know whether and how these trait dimensions are connected.

METHODS

Based on a trait dataset compiled on 131 plant species from 141 studies in flooded habitats, we quantitatively analysed how flooding-induced traits are positioned in relation to the other two dominant trait dimensions: leaf economics traits and size-related traits. We evaluated how these key trait components are expressed along wetness gradients, across habitat types and among plant life forms.

KEY RESULTS

We found that flooding-induced traits constitute a trait dimension independent from leaf economics traits and size-related traits, indicating that there is no generic trade-off associated with flooding adaptations. Moreover, individual flooding-induced traits themselves are to a large extent decoupled from each other. These results suggest that adaptation to stressful environments, such as flooding, can be stressor specific without generic adverse effects on plant functioning (e.g. causing trade-offs on leaf economics traits).

CONCLUSIONS

The trait expression across multiple dimensions promotes plant adaptations and coexistence across multifaceted flooded environments. The decoupled trait dimensions, as related to different environmental drivers, also explain why ecosystem functioning (including, for example, methane emissions) are species and habitat specific. Thus, our results provide a backbone for applying trait-based approaches in wetland ecology by considering flooding-induced traits as an independent trait dimension.

Trapped between drowning and desiccation: Riverine plants under hydropeaking

Hydropeaking is part of hydropower production. The discontinuous release of turbined water during hydropeaking generates sudden rise and falls of the water levels, as well as extended droughts. These artificial flow fluctuations impose challenging growing conditions for riverine vegetation. In order to identify vulnerable/resistant plant species to hydropeaking and to evaluate the impact of contrasting hydropeaking scenarios (simplified (i.e., sudden deep floods, frequent soil saturation and drought) and real-life, power plant-induced scenarios), we measured germination, survival, and morphological and physiological attributes of a selection of 14 plant species commonly found along riparian areas. Species were subject to different hydropeaking scenarios during three months (vegetative period) in the field and in a greenhouse. Half of the species performed worse under hydropeaking in comparison to the control (e.g., less germination and biomass, lower growth rates, reduced stem and root length, physiological stress) but none of the tested hydropeaking scenarios was clearly more disruptive than others. Betula pubescens, Alnus incana and Filipendula ulmifolia showed the largest vulnerability to hydropeaking, while other species (e.g., Carex acuta) were resistant to it. Both in the field and in the greenhouse, plants in perturbed scenarios accumulated more ¹³C than in the control scenario indicating limited capacity to perform ¹³C isotope discrimination and evidencing plant physiological stress. The highest ¹³C abundances were found under drought or flooding conditions in the greenhouse, and under the highest hydropeaking intensities in the field (e.g., Betula pubescens). Our results suggest that any hydropeaking scheme can be equally detrimental in terms of plant performance. Hydropeaking schemes that combine periods of severe drought with long and frequent flooding episodes may create a hostile environment for riverine species. Further research on "hydropeaking-tolerant" plant traits is key to draw the boundaries beyond which riverine species can germinate, grow and complete their life cycle under hydropeaking.

Differential Growth Responses of Alternanthera philoxeroides as Affected by Submergence Depths

Global climate change has resulted in an increase in intensity and frequency of flooding, plants living in lowlands, and shore areas have to confront submergence caused by flooding, submergence-tolerant plants usually respond by adopting either escape or quiescence strategies. While certain plants exhibit a changeover from escape strategy upon partial submergence to quiescence strategy under complete shallow submergence, it remains unknown whether plants completely submerged at different water depths would adjust their strategies to cope with the change in submergence depth. Alternanthera philoxeroides is an ideal species to explore this adjustment as it is widely distributed in flood-disturbed habitats and exhibits an escape strategy when completely submerged in shallow waters. We investigated the responses of A. philoxeroides in terms of morphology, anatomy, and non-structural carbohydrate metabolism by conducting experiments using a series of submergence depths (0, 2, 5, and 9 m). During the submergence treatment, environmental factors such as light, dissolved oxygen, and temperature for submerged plants were kept constant. The results showed that A. philoxeroides plants submerged at depth of 2 m presented an escape strategy via fast stem elongation, extensive pith cavity development, and small biomass loss. However, the retarded stem elongation, reduced pith cavity transverse area, and increased biomass loss along the water depth gradient indicated that A. philoxeroides altered its growth response as water depth increased from 2 to 9 m. It is found that the changeover of response strategies occurred at higher submergence depths (5-9 m). Based on the results of our experiments, we demonstrated that water depth played an important role in driving the change in strategy. The water-depth-dependent growth performance of A. philoxeroides would benefit the species in habit exploration and exploitation. Further studies should focus on the performances of plants when submerged at varied water depths with different light climates and dissolved oxygen content, and how water depths drive the response behaviors of the submerged plants.

Research Status and Trends of Underwater Photosynthesis

Underwater photosynthesis is the most important metabolic activity for submerged plants since it could utilize carbon fixation to replenish lost carbohydrates and improve internal aeration by producing O2. The present study used bibliometric methods to quantify the annual number of publications related to underwater photosynthesis. CiteSpace, as a visual analytic software for the literature, was employed to analyze the distribution of the subject categories, author collaborations, institution collaborations, international (regional) collaborations, and cocitation and keyword burst. The results show the basic characteristics of the literature, the main intellectual base, and the main research powers of underwater photosynthesis. Meanwhile, this paper revealed the research hotspots and trends of this field. This study provides an objective and comprehensive analysis of underwater photosynthesis from a bibliometric perspective. It is expected to provide reference information for scholars in related fields to refine the research direction, solve specific scientific problems, and assist scholars in seeking/establishing relevant collaborations in their areas of interest.

The Effects of Edaphic Factors on Riparian Plants in the Middle and Lower Reaches of the Hanjiang River, China

It is important to understand the interactions between soil and plant in riparian zones to ensure ecosystem function. The effects of edaphic factors on plant composition and species diversity were investigated in the middle and lower reaches of the Hanjiang River (MLHR), China. A total of 154 species of herbs were recorded, and vegetation was divided into 32 clusters according to a two-way indicator species analysis (TWINSPAN). Cynodon dactylon and Paspalum distichum were the most common clusters, accounting for 22.7% and 12.5% of total samples, respectively. Hydric and mesic species were dominant in the first and second transects, with mesophytes dominating the third and fourth transects. First transects situated were mainly composed of perennials and annuals, respectively. Perennials in second transects were present in 83% of sites, and perennials in the third and fourth transects were present in 86% of the sites. Margalef richness index (Dma), Simpson dominance diversity index (D), Shannon–Wiener diversity index (H) and Pielou evenness index (Jsw) were higher in the first transects in some sites. The redundancy analysis (RDA) results indicated that soil moisture content was the dominant factor affecting hydrophilic vegetation types, and total nitrogen (TN) and soil organic matter (SOM) were the most critical factors affecting plant life history types and species diversities in this area.

Abscisic acid is required for exodermal suberization to form a barrier to radial oxygen loss in the adventitious roots of rice (Oryza sativa)

To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.

Carbohydrate saving or biomass maintenance: which is the main determinant of the plant's long-term submergence tolerance?

It is hypothesized that plant submergence tolerance could be assessed from the decline of plant biomass due to submergence, as biomass integrates all eco-physiological processes leading to fitness. An alternative hypothesis stated that the consumption rate of carbohydrate is essential in differing tolerance to submergence. In the present study, the responses of biomass, biomass allocation, and carbohydrate content to simulated long-term winter submergence were assessed in four tolerant and four sensitive perennials. The four tolerant perennials occur in a newly established riparian ecosystem created by The Three Gorges Dam, China. They had 100% survival after 120 days' simulated submergence, and had full photosynthesis recovery after 30 days' re-aeration, and the photosynthetic rate was positively related to the growth during the recovery period. Tolerant perennials were characterized by higher carbohydrate levels, compared with the four sensitive perennials (0% survival) at the end of submergence. Additionally, by using a method which simulates posterior estimates, and bootstraps the confidence interval for the difference between strata means, it was found that the biomass response to post-hypoxia, rather than that to submergence, could be a reliable indicator to assess submergence tolerance. Interestingly, the differences of changes in carbohydrate content between tolerant and sensitive perennials during submergence were significant, which were distinct from the biomass response, supporting the hypothesis that tolerant perennials could sacrifice non-vital components of biomass to prioritize the saving of carbohydrates for later recovery. Our study provides some insight into the underlying mechanism(s) of perennials' tolerance to submergence in ecosystems such as temperate wetland and reservoir riparian.

The effects of water control on the survival and growth of Alternanthera philoxeroides in the vegetative reproduction and seedling stages

Alternanthera philoxeroides (Martius) is an infamous invasive alien plant that is widely distributed in aquatic and terrestrial habitats. To investigate the vegetative reproduction, growth, survival strategy, and the function of leaves in fragment of A. philoxeroides under different water conditions, two water control experiments were conducted with different leaf treatments: (1) water control with stolon fragments, and (2) water control with plants. The water control was subjected to five levels: I 30% soil water content, II 70% soil water content, III 97% soil water content, IV water depth of 5 cm, and V water depth of 10 cm in combination with the two leaf treatments, fragments with two leaves and fragments without leaves. Based on the results, A. philoxeroides produced a significantly higher stem length, node number, leaf number, stem biomass, leaf biomass, and total biomass in the 97% soil water content and in treatments with leaves. Additionally, the stem mass ratio increased and the root mass ratio decreased with the increase of the water content. In Exp. 1, the survival rate was the highest in the 97% water content and was 0 in the 30% water content. Therefore, the leaves of stolon fragments contribute to the vegetative reproduction and growth of A. philoxeroides. In response to different water conditions, A. philoxeroides adopts different strategies according to the resource reserves by itself, which are conducive to its survival and widespread occurrence.

Leaf morphology and chlorophyll fluorescence characteristics of mulberry seedlings under waterlogging stress

Because of its high flooding tolerance, in recent years, mulberry has become a tree species that is used in plant restoration in impact zones in reservoir areas. Therefore, 3-year-old potted forage mulberry seedlings were used to investigate the mechanism of mulberry adaptation to flooding stress. An indoor simulated flooding method was adopted to study the morphology of mulberry seedling leaves and the changes in leaf chlorophyll fluorescence parameters and fluorescence imaging under different flooding times and depths. The results showed that the leaves of mulberry seedlings treated with shallow submergence remained healthy during the flooding period, while the leaves of mulberry seedlings treated with half submergence and full submergence showed different degrees of waterlogging symptoms in the middle and late flooding periods and formed adventitious roots at the base of the stem. Most of the chlorophyll fluorescence parameters decreased at the beginning of flooding, but the steady-state degree of closure of PS II reaction centres (1-qP_Lss) increased significantly. In the later stage of flooding, the fluorescence parameters showed relatively stable trends. Based on these results, we conclude that mulberry has high flooding tolerance due to a combination of morphological and physiological responses.

Physiological and transcriptional responses of Phalaris arundinacea under waterlogging conditions

As a high-yielding forage grass, Phalaris arundinacea widely distributed in the Qinghai-Tibet Plateau region of China. To explore physiological and molecular response mechanism of Phalaris arundinacea under waterlogging, we analyzed the biomass and physiological indexes of three locally grown strains under the submerged condition of 10 cm. The material Z0611 showed the strongest waterlogging resistance while the YS showed the weakest performance. Transcriptome sequencing analysis demonstrated that the YS and Z0611 had 17010 and 7566 differently expression genes (DEGs), respectively, which were mainly concentrated in the metabolic process, cell, ribosome, phenylpropanoid biosynthesis pathway in GO and KEGG databases. We also identified a large number of genes involved in carbohydrate metabolism, hormone signaling regulation, transcription factors, antioxidant system, and ethylene signaling. Our research may provide a scientific basis for the restoration of wetland environment on the Qinghai-Tibet Plateau, and lay a foundation for further exploration of the waterlogging resistance genes of Phalaris arundinacea and breeding of new strains resistant with waterlogging stress.

Effects of repetitive submergence on the accumulation and release of nutrient elements in Pinus elliottii seedlings

Pinus elliottii is an evergreen coniferous tree. It is considered a potential species for ecological restoration in the Three Gorges Reservoir Area (TGRA). To classify the effects of different degrees of flooding stress in winter on nutrient accumulation in Pinus elliottii after experiencing early drought stress in summer, simulated water treatments of deep submergence (DS) and moderate submergence (MS) were imposed after the summer drought period. The results indicated that the survival rate of seedlings was 95.3%, and the accumulation trend of the flooded plants was rapid at an average rate of 1.99 ± 0.33% in the early stage of flooding (stage I: 0-7 days), a rapid release rate in the second stage (stage II: 7-60 days), and an average rate of only 0.07 ± 0.04% in the later stage (stage III: 60-150 days). After 150 days of flooding, the leaves of Pinus elliottii released an average of 7.156 ± 0.4 g kg^-1 of organic carbon, 8.839 ± 0.6 g kg^-1 of nitrogen, 0.781 ± 0.1 g kg^-1 of phosphorus, and 2.985 ± 0.3 g kg^-1 of potassium of macroelement content, and an average of 0.201 ± 0.03 g kg^-1 manganese, 0.147 ± 0.04 g kg^-1 iron, 0.002 g kg^-1 copper, and 0.023 g kg^-1 of zinc of microelement contents. Our results also demonstrated that after 150 days of flooding, the C/N, N/P, and C/P ratios of the nutrient element content of Pinus elliottii in the water-level fluctuation zone of the TGRA were 0.810%, 11.32%, and 9.16%, respectively. The absorption and release of nutrients under water flooding are generally divided into three stages: first, the early storage stage (the first stage: 0 to 7 days, optional), then the rapid release (the second stage: 7 to 60 days), and the later stage slow release phase (third stage: 60 to 150 days). Water flooding reduced the contents of C, N, P, and K and affected the absorption of nutrient elements in the plant. At the same time, soluble Mn^{2 +} and Fe^{2 +} over absorbed during flooding could cause toxicity to leaf tissues. At the same time, Pinus elliottii selected to reduce Cu in leaves to ensure that the root has a strong redox capacity and improve nitrogen utilization, thereby preventing the long-term flooding of toxic cations and acid substances. Taken together, our results conclude that increased drought stress can reduce the ability of Pinus elliottii seedlings to withstand flooding stress; the seedlings of Pinus elliottii can maintain their growth by accumulating certain nutrient elements under submerged conditions, which implies that this species would be a suitable candidate for reforestation in the TGRA because of its tolerance to submergence.

Community Trait Responses of Three Dominant Macrophytes to Variations in Flooding During 2011-2019 in a Yangtze River-Connected Floodplain Wetland (Dongting Lake, China)

In lacustrine wetlands connected to rivers, the changes in flood regimes caused by hydrological projects lead to changes in the community traits of dominant macrophytes and, consequently, influence the structure and function of wetland vegetation. However, community trait responses of macrophytes to the timing and duration of flood disturbance have been rarely quantified. In 2011-2019, we investigated plant species diversity, density, and biomass in three dominant macrophyte communities (Carex brevicuspis C.B. Clarke, Miscanthus sacchariflorus (Maxim.) Hackel, and Polygonum hydropiper L.) through monthly field surveys in Dongting Lake wetlands. Partial least squares regressions were used to analyze how the variations in hydrological regimes affected plant community traits. Apparent inter-annual fluctuations in plant community traits were detected during 2011-2019. The species richness and Shannon index of diversity of Miscanthus and Polygonum communities increased, whereas the Shannon index of diversity of Carex community decreased. Variation in flooding had a greater effect on Polygonum and Carex community traits than on Miscanthus community traits. Flooding disturbed all plant communities, especially when the duration and timing varied. Shorter inundation periods caused the biomass of Miscanthus community to decline, and that of Carex and Polygonum communities to increase. Earlier flood recession caused the species richness and Shannon index of diversity of Polygonum and Miscanthus community to increase, and those of Carex community to decrease. These findings imply that shorter inundation durations and earlier flood recession generated by the operation of the Three Gorges Dam have changed the macrophyte growth pattern.

Diversity of plant assemblages dampens the variability of the growing season phenology in wetland landscapes

Background

The functioning of ecosystems is highly variable through space and time. Climatic and edaphic factors are forcing ecological communities to converge, whereas the diversity of plant assemblages dampens these effects by allowing communities’ dynamics to diverge. This study evaluated whether the growing season phenology of wetland plant communities within landscapes is determined by the climatic/edaphic factors of contrasted regions, by the species richness of plant communities, or by the diversity of plant assemblages. From 2013 to 2016, we monitored the phenology and floristic composition of 118 wetland plant communities across five landscapes distributed along a gradient of edaphic and climatic conditions in the Province of Québec, Canada.

Results

The growing season phenology of wetlands was driven by differences among plant assemblage within landscapes, and not by the species richness of each individual community (< 1% of the explained variation). Variation in the growing season length of wetlands reflected the destabilizing effect of climatic and edaphic factors on green-up dates, which is opposed to the dampening effect of plant assemblage diversity on green-down dates.

Conclusions

The latter dampening effect may be particularly important in the context of increasing anthropogenic activities, which are predicted to impair the ability of wetlands to adapt to fluctuating environmental conditions. Our findings suggest that stakeholders should not necessarily consider local species-poor plant communities of lower conservation value to the global functioning of wetland ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01817-6.

Responses of Swamp Cypress (Taxodium distichum) and Chinese Willow (Salix matsudana) Roots to Periodic Submergence in Mega-Reservoir: Changes in Organic Acid Concentration

Organic acids are critical as secondary metabolites for plant adaption in a stressful situation. Oxalic acid, tartaric acid, and malic acid can improve plant tolerance under waterlogged conditions. Two prominent woody species (Taxodium distichum-Swamp cypress and Salix matsudana-Chinese willow) have been experiencing long-term winter submergence and summer drought in the Three Gorges Reservoir. The objectives of the present study were to explore the responses of the roots of two woody species during flooding as reflected by root tissue concentrations of organic acids. Potted sample plants were randomly divided into three treatment groups: control, moderate submergence, and deep submergence. The concentrations of oxalic acid, tartaric acid, and malic acid in the main root and lateral roots of the two species were determined at four stages. The results showed that T. distichum and S. matsudana adapted well to the water regimes of the reservoir, with a survival rate of 100% during the experiment period. After experiencing a cycle of submergence and emergence, the height and base diameter of the two species showed increasing trends. Changes in base diameter showed insignificant differences between submergence treatments, and only height was significant under deep submergence. The concentrations of three organic acids in the roots of two species were influenced by winter submergence. After emergence in spring, two species could adjust their organic acid metabolisms to the normal level. Among three organic acids, tartaric acid showed the most sensitive response to water submergence, which deserved more studies in the future. The exotic species, T. distichum, had a more stable metabolism of organic acids to winter flooding. However, the native species, S. matsudana, responded more actively to long-term winter flooding. Both species can be considered in vegetation restoration, but it needs more observations for planting around 165 m above sea level, where winter submergence is more than 200 days.

Root biomass and root traits of Alnus glutinosa show size-dependent and opposite patterns in a drained and a rewetted forest peatland

BACKGROUND AND AIMS

Forest peatlands represent 25 % of global peatlands and store large amounts of carbon (C) as peat. Traditionally they have been drained in order to increase forestry yield, which may cause large losses of C from the peat. Rewetting aims to stop these losses and to restore the initial storage function of the peatlands. As roots represent major peat-forming elements in these systems, we sampled roots with diameter <5 mm in a drained and a rewetted forest peatland in north-east Germany to evaluate differences in tree biomass investments below ground, root functional characteristics and root age.

METHODS

We cored soil next to Alnus glutinosa stems and sorted root biomass into <1, 1-2 and 2-5 mm diameter classes. We measured biomass distribution and specific root area (SRA) in 10-cm depth increments down to 50 cm, and estimated root age from annual growth rings.

KEY RESULTS

Root biomass in the rewetted site was more than double that in the drained site. This difference was mostly driven by very fine roots <1 mm, which accounted for 51 % of the total root biomass and were mostly (75 %) located in the upper 20 cm. For roots <1 mm, SRA did not differ between the sites. However, SRA of the 1-2 mm and 2-5 mm diameter roots was higher in the drained than in the rewetted site. Root age did not differ between sites.

CONCLUSIONS

The size-dependent opposite patterns between root biomass and their functional characteristics under contrasting water regimes indicate differences between fine and coarse roots in their response to environmental changes. Root age distribution points to similar root turnover rates between the sites, while higher root biomass in the rewetted site clearly indicates larger tree C stocks below ground under rewetting, supporting the C sink function of the ecosystem.

Tolerance to excess moisture in soybean is enhanced by over-expression of the Glycine max Phytoglobin (GmPgb1)

Excess moisture in the form of waterlogging or full submergence can cause severe conditions of hypoxia or anoxia compromising several physiological and biochemical processes. A decline in photosynthetic rate due to accumulation of ROS and damage of leaf tissue are the main consequences of excess moisture. These effects compromise crop yield and quality, especially in sensitive species, such as soybean (Glycine max.). Phytoglobins (Pgbs) are expressed during hypoxia and through their ability to scavenge nitric oxide participate in several stress-related responses. Soybean plants over-expressing or suppressing the Pgb1 gene GmPgb1 were generated and their ability to cope with waterlogging and full submergence conditions was assessed. Plants over-expressing GmPgb1 exhibited a higher retention of photosynthetic rate during waterlogging and survival rate during submergence relative to wild type plants. The same plants also had lower levels of ROS due to a reduction in expression of Respiratory Burst Oxidase Homologs (RBOH), components of the NADPH oxidase enzyme, and enhanced antioxidant system characterized by higher expression of catalases (CAT) and superoxide dismutase (SOD), as well as elevated expression and activity of ascorbate peroxidase (APX). Plants over-expressing GmPgb1 also exhibited an expression pattern of aquaporins typical of excess moisture resilience. This was in contrast to plants downregulating GmPgb1 which were characterized by the lowest photosynthetic rates, higher ROS signal, and reduced expression and activities of many antioxidant enzymes. Results from these studies suggest that GmPgb1 exercises a protective role during conditions of excess moisture with similar mechanisms operating during waterlogging and submergence.

Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans

Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m² s at 0.5 m to 7.9 μmol/m² s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared with those grown in the aquaria. Our results suggest that the bottom mud of the pond is not the major limiting factor in the re-establishment of V. natans. Because water depth and light attenuation exerted strong stress on V. natans, shallow areas or measures to improve water transparency are required to promote the introduction of V. natans in eutrophic ponds for successful restoration in urban areas.

Submergence deactivates wound-induced plant defence against herbivores

Flooding is a common and critical disaster in agriculture, because it causes defects in plant growth and even crop loss. An increase in herbivore populations is often observed after floods, which leads to additional damage to the plants. Although molecular mechanisms underlying the plant responses to flooding have been identified, how plant defence systems are affected by flooding remains poorly understood. Herein, we show that submergence deactivates wound-induced defence against herbivore attack in Arabidopsis thaliana. Submergence rapidly suppressed the wound-induced expression of jasmonic acid (JA) biosynthesis genes, resulting in reduced JA accumulation. While plants exposed to hypoxia in argon gas exhibited similar reduced wound responses, the inhibitory effects were initiated after short-term submergence without signs for lack of oxygen. Instead, expression of ethylene-responsive genes was increased after short-term submergence. Blocking ethylene signalling by ein2-1 mutation partially restored suppressed expression of several wound-responsive genes by submergence. In addition, submergence rapidly removed active markers of histone modifications at a gene locus involved in JA biosynthesis. Our findings suggest that submergence inactivates defence systems of plants, which would explain the proliferation of herbivores after flooding.

Hyo-Jun Lee et al. show that submergence in Arabidopsis deactivates wound-induced defence against herbivore attack by suppressing the expression of jasmonic acid biosynthesis genes and increasing expression of ethylene-responsive genes. These results shed light on how flooding may impact plant defence systems.

Wetter is Better: Rewetting of Minerotrophic Peatlands Increases Plant Production and Moves Them Towards Carbon Sinks in a Dry Year

Peatlands are effective carbon sinks as more biomass is produced than decomposed under the prevalent anoxic conditions. Draining peatlands coupled with warming releases stored carbon, and subsequent rewetting may or may not restore the original carbon sink. Yet, patterns of plant production and decomposition in rewetted peatlands and how they compare to drained conditions remain largely unexplored. Here, we measured annual above- and belowground biomass production and decomposition in three different drained and rewetted peatland types: alder forest, percolation fen and coastal fen during an exceptionally dry year. We also used standard plant material to compare decomposition between the sites, regardless of the decomposability of the local plant material. Rewetted sites showed higher root and shoot production in the percolation fen and higher root production in the coastal fen, but similar root and leaf production in the alder forest. Decomposition rates were generally similar in drained and rewetted sites, only in the percolation fen and alder forest did aboveground litter decompose faster in the drained sites. The rewetted percolation fen and the two coastal sites had the highest projected potential for organic matter accumulation. Roots accounted for 23–66% of total biomass production, and belowground biomass, rather than aboveground biomass, was particularly important for organic matter accumulation in the coastal fens. This highlights the significance of roots as main peat-forming element in these graminoid-dominated fen peatlands and their crucial role in carbon cycling, and shows that high biomass production supported the peatlands’ function as carbon sink even during a dry year.

The Anaerobic Product Ethanol Promotes Autophagy-Dependent Submergence Tolerance in Arabidopsis

In response to hypoxia under submergence, plants switch from aerobic respiration to anaerobic fermentation, which leads to the accumulation of the end product, ethanol. We previously reported that Arabidopsis thaliana autophagy-deficient mutants show increased sensitivity to ethanol treatment, indicating that ethanol is likely involved in regulating the autophagy-mediated hypoxia response. Here, using a transcriptomic analysis, we identified 3909 genes in Arabidopsis seedlings that were differentially expressed in response to ethanol treatment, including 2487 upregulated and 1422 downregulated genes. Ethanol treatment significantly upregulated genes involved in autophagy and the detoxification of reactive oxygen species. Using transgenic lines expressing AUTOPHAGY-RELATED PROTEIN 8e fused to green fluorescent protein (GFP-ATG8e), we confirmed that exogenous ethanol treatment promotes autophagosome formation in vivo. Phenotypic analysis showed that deletions in the alcohol dehydrogenase gene in adh1 mutants result in attenuated submergence tolerance, decreased accumulation of ATG proteins, and diminished submergence-induced autophagosome formation. Compared to the submergence-tolerant Arabidopsis accession Columbia (Col-0), the submergence-intolerant accession Landsberg erecta (Ler) displayed hypersensitivity to ethanol treatment; we linked these phenotypes to differences in the functions of ADH1 and the autophagy machinery between these accessions. Thus, ethanol promotes autophagy-mediated submergence tolerance in Arabidopsis.