Ethylene-Mediated Acclimations to Flooding Stress

Root-zone oxygen supply mitigates waterlogging stress in tomato by enhancing root growth, photosynthetic performance, and antioxidant capacity

Water-air coupled oxygen supply to the root zone can significantly enhance crop yield and quality under non-waterlogged conditions. However, its impact on crops subjected to waterlogging-induced hypoxia remains unclear. In this study, tomatoes were chosen as the model crop due to their economic value and sensitivity to waterlogged conditions. Two tomato cultivars, "Micro-Tom" and "Omanda-3," were subjected to waterlogging and treated with varying levels of water-air coupled oxygen supply. The results demonstrated that supplying 25 mL or 50 mL of air per plant to the root zone significantly improved biomass compared to waterlogged plants without additional oxygen. Notably, root dry weight increased by over 73.0% in both varieties. Root morphological analysis revealed that oxygen supply in the root zone greatly promoted root growth, with marked increases in surface area (149.7%), root length (181.2%), fork number (198.4%), and tip number (165.4%). Furthermore, photosynthesis and antioxidant assays showed substantial increases in the leaf net photosynthetic rate, transpiration rate, stomatal conductance, as well as catalase and peroxidase activity in response to oxygen supply. Consequently, fruit yield increased by 86.2% in Micro-Tom and 24.3% in Omanda-3. In conclusion, oxygen supplementation through the water-air coupling technique effectively enhanced root growth, photosynthesis, and antioxidant capacity in waterlogged tomato plants, alleviating hypoxic stress and associated yield losses. These findings offer a theoretical basis and practical recommendations for managing waterlogged farmland in diverse agricultural contexts.

Mechanisms of plant acclimation to multiple abiotic stresses

Plants frequently encounter a range of abiotic stresses and their combinations. Even though stresses rarely occur in isolation, research on plant stress resilience typically focuses on single environmental stressors. Plant responses to abiotic stress combinations are often distinct from corresponding individual stresses. Factors determining the outcomes of combined stresses are complex and multifaceted. In this review, we summarize advancements in our understanding of the mechanisms underlying plant responses to co-occurring (combined and sequential) abiotic stresses, focusing on morphological, physiological, developmental, and molecular aspects. Comprehensive understanding of plant acclimation, including the signaling and response mechanisms to combined and individual stresses, can contribute to the development of strategies for enhancing plant resilience in dynamic environments.

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

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

Genome-Wide Identification, Characterization, and Expression Analysis of the BTB domain-Containing Protein Gene Family in Poplar

In recent years, the BTB (Bric-a-brac/Tramtrack/Broad complex) gene family in plants has garnered widespread attention for its regulatory roles in plant growth and development. However, knowledge regarding BTBs in poplar trees remains limited. Here, we identified 94 BTB gene family members across the genome of Populus alba L. Through phylogenetic analysis, these members were classified into seven subfamilies and 16 branches, followed by comprehensive bioinformatics and biological analyses. Structural analysis revealed that poplar BTB gene family exhibits both high conservation and diversity, with distinct gene structures and protein features. Expression pattern analysis demonstrated differential expression of poplar BTB genes across various tissues, hormone treatments, and under drought stress, suggesting their potential roles in poplar growth and development and drought response. This study provides a vital foundation and reference for unraveling the BTB-involved regulatory mechanisms underlying poplar growth and development and drought response.

CmHRE2L-CmACS6 transcriptional cascade negatively regulates waterlogging tolerance in Chrysanthemum

The role of ethylene as an initial signaling molecule in waterlogging stress is well-established. However, the complex molecular mechanisms underlying ethylene biosynthesis and its functional significance in chrysanthemums under waterlogging conditions have remained unclear. In this study, we observed an increase in the expression of 1-aminocyclopropane-1-carboxylate synthase 6 (CmACS6), which encodes a key enzyme responsible for ethylene biosynthesis, in response to waterlogging. This elevation increases ethylene production, induces leaf chlorosis, and enhances the chrysanthemum's sensitivity to waterlogging stress. Moreover, our analysis of upstream regulators revealed that the expression of CmACS6, in response to waterlogging, is directly upregulated by CmHRE2-like (Hypoxia Responsive ERF-like, CmHRE2L), an ethylene response factor. Notably, CmHRE2-L binds directly to the GCC-like motif in the promoter region of CmACS6. Genetic validation assays demonstrated that CmHRE2L was induced by waterlogging and contributed to ethylene production, consequently reducing waterlogging tolerance in a partially CmACS6-dependent manner. This study identified the regulatory module involving CmHRE2L and CmACS6, which governs ethylene biosynthesis in response to waterlogging stress.

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

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

Waterlogging stress mechanism and membrane transporters in soybean (Glycine max (L.) Merr.)

An excess of water is more harmful to plant growth, root growth and the uniformity of the plant population than a water deficit. Water is a crucial factor in the three basic stages of soybean development: germination, emergence and flowering/seed filling. Waterlogging is one of the biggest constraints to crop production and productivity in India and can occur at any stage in soybean. However, seeds and seedlings are damaged by waterlogging resulting in a significant reduction in grain yield. Seed yield and growth are significantly correlated at the seedling stage. In addition, the plant is under constant pressure due to changing environmental conditions and has difficulty withstanding these harsh, unpredictable and difficult situations. Membrane transporters are essential and play fundamental roles during waterlogging thereby facilitating cellular homeostasis and gaseous exchange, which support plant growth and development. This review highlights the genetic basis and mechanism of waterlogging tolerance in soybean and the role of climate in influencing the genetic makeup of the crop, paving the way for further development of improved soybean varieties. Simultaneously, the article highlights membrane transporters' importance in water-mediated stress in soybeans.

A comprehensive analytical method 'Regulatome' revealed a novel pathway for aerenchyma formation under waterlogging in wheat

Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation is one of the most important adaptive strategies in waterlogging-tolerant plants. However, the conservation of this process remains poorly understood, and additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, and metabolomic analyses were conducted on wheat seedlings under normal and waterlogging conditions. Waterlogging caused growth inhibition and physiological damage, as well as induced aerenchyma formation in roots. A total of 10,346 differentially expressed genes and 3,419 differential metabolites were identified in roots. In addition to the AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating analyses also revealed the role of LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) in aerenchyma formation under waterlogging. It was revealed that the classical pathway of aerenchyma formation mediated by ethylene response, as well as synergy of calcium ion and reactive oxygen species, was deeply conserved in both monocots and eudicots during 160 million years of evolution through gene co-expression networks of cross-species. The newly introduced concept 'Regulatome' supported the classical pathway of aerenchyma formation, with a proposed model of the jasmonic acid signalling pathway involved in waterlogging, suggesting its usefulness in gene identification and function exploration. These findings provide a novel insight into the regulatory mechanisms of aerenchyma formation and breeding approaches for developing wheat cultivars with high waterlogging tolerance.

Genetic variations in ZmEREB179 are associated with waterlogging tolerance in maize

Maize (Zea mays) is highly susceptible to waterlogging stress, which reduces both the yield and quality of this important crop. However, the molecular mechanism governing waterlogging tolerance is poorly understood. In this study, we identify a waterlogging- and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor (ERF) localized in the nucleus. Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress. Conversely, the zmereb179 knockout mutants are more tolerant to waterlogging, suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance. A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes, including ZmEREB180. We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression. Notably, the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter (Hap2) are highly associated with waterlogging resistance. The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations, highlighting its potential applications in breeding programs. Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.

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

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

Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing

Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.

Calcium signaling triggers early high humidity responses in Arabidopsis thaliana

Plants need to adapt to fluctuating atmospheric humidity and respond to both high and low humidity. Despite our substantial understanding of plant responses to low humidity, molecular mechanisms underlying the high humidity (HH) response are much less well understood. In this study, we investigated early responses to HH in Arabidopsis. Expression of CYP707A3, encoding an abscisic acid (ABA) 8'-hydroxylase, is induced by HH within 10 min, which leads to a decrease in foliar ABA level. We identified that the combined action of CAMTA3 and CAMTA2 transcription factors regulate this response. This regulation requires a calmodulin (CaM)-binding domain of CAMTA3. Transcriptomes of HH-regulated genes are enriched in those related to calcium signaling, including cyclic nucleotide-gated ion channels (CNGCs). Moreover, HH induces CNGC2- and CNGC4-mediated increases in cytosolic Ca2+ concentrations in leaves within a few minutes. We also found that CNGC2, CNGC4, and CAMTAs participate in HH-induced hyponastic movement of petioles. Taken together, our results indicate that CNGC2/CNGC4-Ca2+-CaM-CAMTA3/CAMTA2 acts as a primary regulatory module to trigger downstream HH responses.

The role of ethylene in the regulation of plant response mechanisms to waterlogging stress

Waterlogging stands as a common environmental challenge, significantly affecting plant growth, yield, and, in severe cases, survival. In response to waterlogging stress, plants exhibit a series of intricate physiologic, metabolic, and morphologic adaptations. Notably, the gaseous phytohormone ethylene is rapidly accumulated in the plant submerged tissues, assuming an important regulatory factor in plant-waterlogging tolerance. In this review, we summarize recent advances in research on the mechanisms of ethylene in the regulation of plant responses to waterlogging stress. Recent advances found that both ethylene biosynthesis and signal transduction make indispensable contributions to modulating plant adaptation mechanisms to waterlogged condition. Ethylene was also discovered to play an important role in plant physiologic metabolic responses to waterlogging stress, including the energy mechanism, morphologic adaptation, ROS regulation and interactions with other phytohormones. The comprehensive exploration of ethylene and its associated genes provides valuable insights into the precise strategies to leverage ethylene metabolism for enhancing plant resistance to waterlogging stress.

Phylotranscriptomics provides a treasure trove of flood-tolerance mechanisms in the Cardamineae tribe

Flooding events are highly detrimental to most terrestrial plant species. However, there is an impressive diversity of plant species that thrive in flood-prone regions and represent a treasure trove of unexplored flood-resilience mechanisms. Here we surveyed a panel of four species from the Cardamineae tribe representing a broad tolerance range. This included the flood-tolerant Cardamine pratensis, Rorippa sylvestris and Rorippa palustris and the flood-sensitive species Cardamine hirsuta. All four species displayed a quiescent strategy, evidenced by the repression of shoot growth underwater. Comparative transcriptomics analyses between the four species and the sensitive model species Arabidopsis thaliana were facilitated via de novo transcriptome assembly and identification of 16 902 universal orthogroups at a high resolution. Our results suggest that tolerance likely evolved separately in the Cardamine and Rorippa species. While the Rorippa response was marked by a strong downregulation of cell-cycle genes, Cardamine minimized overall transcriptional regulation. However, a weak starvation response was a universal trait of tolerant species, potentially achieved in multiple ways. It could result from a strong decline in cell-cycle activity, but is also intertwined with autophagy, senescence, day-time photosynthesis and night-time fermentation capacity. Our data set provides a rich source to study adaptational mechanisms of flooding tolerance.

Genome-wide identification of the EIN3/EIL transcription factor family and their responses under abiotic stresses in Medicago sativa

BACKGROUND

Medicago sativa, often referred to as the "king of forage", is prized for its high content of protein, minerals, carbohydrates, and digestible nutrients. However, various abiotic stresses can hinder its growth and development, ultimately resulting in reduced yield and quality, including water deficiency, high salinity, and low temperature. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) transcription factors are key regulators in the ethylene signaling pathway in plants, playing crucial roles in development and in the response to abiotic stresses. Research on the EIN3/EIL gene family has been reported for several species, but minimal information is available for M. sativa.

RESULTS

In this study, we identified 10 MsEIN3/EIL genes from the M. sativa genome (cv. Zhongmu No.1), which were classified into three clades based on phylogenetic analysis. The conserved structural domains of the MsEIN3/EIL genes include motifs 1, 2, 3, 4, and 9. Gene duplication analyses suggest that segmental duplication (SD) has played a significant role in the expansion of the MsEIN3/EIL gene family throughout evolution. Analysis of the cis-acting elements in the promoters of MsEIN3/EIL genes indicates their potential to respond to various hormones and environmental stresses. We conducted a further analysis of the tissue-specific expression of the MsEIN3/EIL genes and assessed the gene expression profiles of MsEIN3/EIL under various stresses using transcriptome data, including cold, drought, salt and abscisic acid treatments. The results showed that MsEIL1, MsEIL4, and MsEIL5 may act as positive regulatory factors involved in M. sativa's response to abiotic stress, providing important genetic resources for molecular design breeding.

CONCLUSION

This study investigated MsEIN3/EIL genes in M. sativa and identified three candidate transcription factors involved in the regulation of abiotic stresses. These findings will offer valuable insights into uncovering the molecular mechanisms underlying various stress responses in M. sativa.

Dissecting negative effects of two root-associated bacteria on the growth of an invasive weed

Plant-associated microorganisms can negatively influence plant growth, which makes them potential biocontrol agents for weeds. Two Gammaproteobacteria, Serratia plymuthica and Pseudomonas brassicacearum, isolated from roots of Jacobaea vulgaris, an invasive weed, negatively affect its root growth. We examined whether the effects of S. plymuthica and P. brassicacearum on J. vulgaris through root inoculation are concentration-dependent and investigated if these effects were mediated by metabolites in bacterial suspensions. We also tested whether the two bacteria negatively affected seed germination and seedling growth through volatile emissions. Lastly, we investigated the host specificity of these two bacteria on nine other plant species. Both bacteria significantly reduced J. vulgaris root growth after root inoculation, with S. plymuthica showing a concentration-dependent pattern in vitro. The cell-free supernatants of both bacteria did not affect J. vulgaris root growth. Both bacteria inhibited J. vulgaris seed germination and seedling growth via volatiles, displaying distinct volatile profiles. However, these negative effects were not specific to J. vulgaris. Both bacteria negatively affect J. vulgaris through root inoculation via the activity of bacterial cells, while also producing volatiles that hinder J. vulgaris germination and seedling growth. However, their negative effects extend to other plant species, limiting their potential for weed control.

Hypoxia reshapes Arabidopsis root architecture by integrating ERF-VII factor response and abscisic acid homoeostasis

Oxygen limitation (hypoxia), arising as a key stress factor due to flooding, negatively affects plant development. Consequently, maintaining root growth under such stress is crucial for plant survival, yet we know little about the root system's adaptions to low-oxygen conditions and its regulation by phytohormones. In this study, we examine the impact of hypoxia and, herein, the regulatory role of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors on root growth in Arabidopsis. We found lateral root (LR) elongation to be actively maintained by hypoxia via ERFVII factors, as erfVII seedlings possess hypersensitivity towards hypoxia regarding their LR growth. Pharmacological inhibition of abscisic acid (ABA) biosynthesis revealed ERFVII-driven counteraction of hypoxia-induced inhibition of LR formation in an ABA-dependent manner. However, postemergence LR growth under hypoxia mediated by ERFVIIs was independent of ABA. In roots, ERFVIIs mediate, among others, the induction of ABA-degrading ABA 8'-hydroxylases CYP707A1 expression. RAP2.12 could activate the pCYC707A1:LUC reporter gene, indicating, combined with single mutant analyses, that this transcription factor regulates ABA levels through corresponding transcript upregulation. Collectively, hypoxia-induced adaptation of the Arabidopsis root system is shaped by developmental reprogramming, whereby ERFVII-dependent promotion of LR emergence, but not elongation, is partly executed through regulation of ABA degradation.

High expression of ethylene response factor BcERF98 delays the flowering time of non-heading Chinese cabbage

MAIN CONCLUSION

BcERF98 is induced by ethylene signaling and inhibits the expression of BcFT by interacting with BcNF-YA2 and BcEIP9, thereby inhibiting plant flowering. Several stresses trigger the accumulation of ethylene, which then transmits the signal to ethylene response factors (ERFs) to participate in the regulation of plant development to adapt to the environment. This study clarifies the function of BcERF98, a homolog of AtERF98, in the regulation of plant flowering time mediated by high concentrations of ethylene. Results indicate that BcERF98 is a nuclear and the cell membrane-localized transcription factor and highly responsive to ethylene signaling. BcERF98 inhibits the expression of BcFT by interacting with BcEIP9 and BcNF-YA2, which are related to flowering time regulation, thereby participating in ethylene-mediated plant late flowering regulation. The results have enriched the theoretical knowledge of flowering regulation in non-heading Chinese cabbage (NHCC), providing the scientific basis and gene reserves for cultivating new varieties of NHCC with different flowering times.

Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1

The phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, ethylene quickly increases to high concentrations owing to its low solubility and diffusion rates in water. Ethylene accumulation in submerged plant tissues makes it a reliable cue for triggering flood acclimation responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers photosynthetic capacity and stress recovery. In submerged Arabidopsis, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid indiscriminate breakdown of leaves despite high systemic ethylene accumulation. We demonstrate that although submergence triggers leaf-age-independent activation of ethylene signaling via EIN3 in Arabidopsis, senescence is initiated only in old leaves. EIN3 stabilization also leads to overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1) in both old and young leaves during submergence. However, leaf-age-dependent senescence can be explained by ORE1 protein activation via phosphorylation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. A systematic analysis of the roles of the major flooding stress cues and signaling pathways shows that only the combination of ethylene and darkness is sufficient to mimic submergence-induced senescence involving ORE1 accumulation and phosphorylation. Hypoxia, most often associated with flooding stress in plants, appears to have no role in these processes. Our results reveal a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses such as flooding. Age-dependent ORE1 activity ensures that older, expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues that are vital to whole-plant survival.

Ethylene: A Modulator of the Phytohormone-Mediated Insect Herbivory Network in Plants

Plants have evolved to establish insect herbivory defences by modulating their metabolism, growth, and development. Precise networks of phytohormones are essential to induce those herbivory defences. Gaseous phytohormone ET plays an important role in forming herbivory defences. Its role in insect herbivory is not fully understood, but previous studies have shown that it can both positively and negatively regulate herbivory. This review presents recent findings on crosstalk between ET and other phytohormones in herbivory responses. Additionally, the use of exogenous ETH treatment to induce ET in response to herbivory is discussed.

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

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

Unraveling Key Factors for Hypoxia Tolerance in Contrasting Varieties of Cotton Rose by Comparative Morpho-physiological and Transcriptome Analysis

The cotton rose (Hibiscus mutabilis) is a plant species commonly found in tropical and subtropical regions. It is remarkably resilient to waterlogging stress; however, the underlying mechanism behind this trait is yet unknown. This study used hypoxia-tolerant "Danbanhong" (DBH) and more hypoxia-sensitive "Yurui" (YR) genotypes and compared their morpho-physiological and transcriptional responses to hypoxic conditions. Notably, DBH had a higher number of adventitious roots (20.3) compared to YR (10.0), with longer adventitious roots in DBH (18.3 cm) than in YR (11.2 cm). Furthermore, the formation of aerenchyma was 3-fold greater in DBH compared to YR. Transcriptomic analysis revealed that DBH had more rapid transcriptional responses to hypoxia than YR. Identification of a greater number of differentially expressed genes (DEGs) for aerenchyma, adventitious root formation and development, and energy metabolism in DBH supported that DBH had better morphological and transcriptional adaptation than YR. DEG functional enrichment analysis indicated the involvement of variety-specific biological processes in adaption to hypoxia. Plant hormone signaling transduction, MAPK signaling pathway and carbon metabolism played more pronounced roles in DBH, whereas the ribosome genes were specifically induced in YR. These results show that effective multilevel coordination of adventitious root development and aerenchyma, in conjunction with plant hormone signaling and carbon metabolism, is required for increased hypoxia tolerance. This study provides new insights into the characterization of morpho-physiological and transcriptional responses to hypoxia in H. mutabilis, shedding light on the molecular mechanisms of its adaptation to hypoxic environments.

Transcriptome analysis of waterlogging-induced adventitious root and control taproot of Mentha arvensis

KEY MESSAGE

The present study reports differentially expressed transcripts in the waterlogging-induced adventitious root (AR) of Mentha arvensis; the identified transcripts will help to understand AR development and improve waterlogging stress response. Waterlogging notably hampers plant growth in areas facing waterlogged soil conditions. In our previous findings, Mentha arvensis was shown to adapt better in waterlogging conditions by initiating the early onset of adventitious root development. In the present study, we compared the transcriptome analysis of adventitious root induced after the waterlogging treatment with the control taproot. The biochemical parameters of total carbohydrate, total protein content, nitric oxide (NO) scavenging activity and antioxidant enzymes, such as catalase activity (CAT) and superoxide dismutase (SOD) activity, were enhanced in the adventitious root compared with control taproot. Analysis of differentially expressed genes (DEGs) in adventitious root compared with the control taproot were grouped into four functional categories, i.e., carbohydrate metabolism, antioxidant activity, hormonal regulation, and transcription factors that could be majorly involved in the development of adventitious roots. Differential expression of the upregulated and uniquely expressing thirty-five transcripts in adventitious roots was validated using qRT-PCR. This study has generated the resource of differentially and uniquely expressing transcripts in the waterlogging-induced adventitious roots. Further functional characterization of these transcripts will be helpful to understand the development of adventitious roots, leading to the resistance towards waterlogging stress in Mentha arvensis.

Identification of Key Ubiquitination Sites Involved in the Proteasomal Degradation of AtACS7 in Arabidopsis

The gaseous hormone ethylene plays pivotal roles in plant growth and development. The rate-limiting enzyme of ethylene biosynthesis in seed plants is 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS). ACS proteins are encoded by a multigene family and the expression of ACS genes is highly regulated, especially at a post-translational level. AtACS7, the only type III ACS in Arabidopsis, is degraded in a 26S proteasome-dependent pathway. Here, by using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis, two lysine residues of AtACS7, lys285 (K285) and lys366 (K366), were revealed to be ubiquitin-modified in young, light-grown Arabidopsis seedlings but not in etiolated seedlings. Deubiquitylation-mimicking mutations of these residues significantly increased the stability of the AtACS7K285RK366R mutant protein in cell-free degradation assays. All results suggest that K285 and K366 are the major ubiquitination sites on AtACS7, providing deeper insights into the post-translational regulation of AtACS7 in Arabidopsis.

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.

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.

Ethylene Modulates Rice Root Plasticity under Abiotic Stresses

Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.

Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1

The world's low-lying rice (Oryza sativa) cultivation areas are under threat of submergence or flash flooding due to global warming. Rice plants manifest a variety of physiological and morphological changes to cope with submergence and hypoxia, including lowering carbohydrate consumption, inhibiting shoot elongation, and forming a thicker leaf gas film during submergence. Functional studies have revealed that submergence tolerance in rice is mainly determined by an ethylene response factor (ERF) transcription factor-encoding gene, namely SUBMERGENCE 1A-1 (SUB1A-1) located in the SUB1 quantitative trait locus. The SUB1A-1-dependent submergence tolerance is manifested through hormonal signaling involving ethylene, gibberellic acid, brassinosteroid, auxin and jasmonic acid. Considerable progress has been made toward the introduction of SUB1A-1 into rice varieties through a conventional marker-assisted backcrossing approach. Here, we review the recent advances in the physiological, biochemical and molecular dynamics of rice submergence tolerance mediated by the 'quiescence strategy'. Thus, the present review aims to provide researchers with insights into the genetics of rice submergence tolerance and future perspectives for designing submergence-resilient plants for sustainable agriculture under the uncertainties of climate change.

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.

Genome-wide identification and characterization of ADH gene family and the expression under different abiotic stresses in tomato (Solanum lycopersicum L.)

The SlADH gene plays a key role in environmental stress response. However, limited studies exist regarding the tomato SlADH gene. In this study, we identified 35 SlADH genes in tomato by genome-wide identification. Among the 12 chromosomes of tomato, SlADH gene is distributed on 10 chromosomes, among which the 7th and 10th chromosomes have no family members, while the 11th chromosome has the most members with 8 family members. Members of this gene family are characterized by long coding sequences, few amino acids, and introns that make up a large proportion of the genetic structure of most members of this family. Moreover, the molecular weight of the proteins of the family members was similar, and the basic proteins were mostly, and the overall distribution was relatively close to neutral (pI = 7). This may indicate that proteins in this family have a more conserved function. In addition, a total of four classes of cis-acting elements were detected in all 35 SlADH promoter regions, most of which were associated with biotic and abiotic stresses. The results indicate that SlADH gene had a certain response to cold stress, salt stress, ABA treatment and PEG stress. This study provides a new candidate gene for improving tomato stress resistance.

CIPK15-mediated inhibition of NH4+ transport protects Arabidopsis from submergence

Ammonium (NH4+) serves as a vital nitrogen source for plants, but it can turn toxic when it accumulates in excessive amounts. Toxicity is aggravated under hypoxic/anaerobic conditions, e.g., during flooding or submergence, due to a lower assimilation capacity. AMT1; 1 mediates NH4+ uptake into roots. Under conditions of oxygen-deficiency, i.e., submergence, the CBL-interacting protein kinase OsCIPK15 has been shown to trigger SnRK1A signaling, promoting starch mobilization, thereby the increasing availability of ATP, reduction equivalents and acceptors for NH4+ assimilation in rice. Our previous study in Arabidopsis demonstrates that AtCIPK15 phosphorylates AMT1; 1 whose activity is under allosteric feedback control by phosphorylation of T460 in the cytosolic C-terminus. Here we show that submergence cause higher NH4+ accumulation in wild-type, plant but not of nitrate, nor in a quadruple amt knock-out mutant. In addition, submergence triggers rapid accumulation of AtAMT1;1 and AtCIPK15 transcripts as well as AMT1 phosphorylation. Significantly, cipk15 knock-out mutants do not exhibit an increase in AMT1 phosphorylation; however, they do display heightened sensitivity to submergence. These findings suggest that CIPK15 suppresses AMT activity, resulting in decreased NH4+ accumulation during submergence, a period when NH4+ assimilation capacity may be impaired.

Aspergillus nomiae and fumigatus Ameliorating the Hypoxic Stress Induced by Waterlogging through Ethylene Metabolism in Zea mays L

Transient and prolonged waterlogging stress (WS) stimulates ethylene (ET) generation in plants, but their reprogramming is critical in determining the plants' fate under WS, which can be combated by the application of symbiotically associated beneficial microbes that induce resistance to WS. The present research was rationalized to explore the potential of the newly isolated 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophytic consortium of Aspergillus nomiae (MA1) and Aspergillus fumigatus (MA4) on maize growth promotion under WS. MA1 and MA4 were isolated from the seeds of Moringa oleifera L., which ably produced a sufficient amount of IAA, proline, phenols, and flavonoids. MA1 and MA4 proficiently colonized the root zone of maize (Zea mays L.). The symbiotic association of MA1 and MA4 promoted the growth response of maize compared with the non-inoculated plants under WS stress. Moreover, MA1- and MA4-inoculated maize plants enhanced the production of total soluble protein, sugar, lipids, phenolics, and flavonoids, with a reduction in proline content and H2O2 production. MA1- and MA4-inoculated maize plants showed an increase in the DPPH activity and antioxidant enzyme activities of CAT and POD, along with an increased level of hormonal content (GA3 and IAA) and decreased ABA and ACC contents. Optimal stomatal activity in leaf tissue and adventitious root formation at the root/stem junction was increased in MA1- and MA4-inoculated maize plants, with reduced lysigenous aerenchyma formation, ratio of cortex-to-stele, water-filled cells, and cell gaps within roots; increased tight and round cells; and intact cortical cells without damage. MA1 and MA4 induced a reduction in deformed mesophyll cells, and deteriorated epidermal and vascular bundle cells, as well as swollen metaxylem, phloem, pith, and cortical area, in maize plants under WS compared with control. Moreover, the transcript abundance of ethylene-responsive gene ZmEREB180, responsible for the induction of the WS tolerance in maize, showed optimally reduced expression sufficient for induction in WS tolerance, in MA1- and MA4-inoculated maize plants under WS compared with the non-inoculated control. The existing research supported the use of MA1 and MA4 isolates for establishing the bipartite mutualistic symbiosis in maize to assuage the adverse effects of WS by optimizing ethylene production.

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.

Parallels between drought and flooding: An integrated framework for plant eco-physiological responses to water stress

Drought and flooding occur at opposite ends of the soil moisture spectrum yet their resulting stress responses in plants share many similarities. Drought limits root water uptake to which plants respond with stomatal closure and reduced leaf gas exchange. Flooding limits root metabolism due to soil oxygen deficiency, which also limits root water uptake and leaf gas exchange. As drought and flooding can occur consecutively in the same system and resulting plant stress responses share similar mechanisms, a single theoretical framework that integrates plant responses over a continuum of soil water conditions from drought to flooding is attractive. Based on a review of recent literature, we integrated the main plant eco-physiological mechanisms in a single theoretical framework with a focus on plant water transport, plant oxygen dynamics, and leaf gas exchange. We used theory from the soil-plant-atmosphere continuum modeling as "backbone" for our framework, and subsequently incorporated interactions between processes that regulate plant water and oxygen status, abscisic acid and ethylene levels, and the resulting acclimation strategies in response to drought, waterlogging, and complete submergence. Our theoretical framework provides a basis for the development of mathematical models to describe plant responses to the soil moisture continuum from drought to flooding.

Functional responses to multiple sequential abiotic stress (waterlogging-drought) in three woody taxa with different root systems and stress tolerance

There is generally a trade-off in the resistance to drought and to waterlogging. However, several species are sequentially subjected to both stressors in many environments. We evaluated the ecophysiological strategies to cope with multiple sequential stress of waterlogging and drought (W + D) of three taxa differing in stress resistance and root morphology: the phreatophic Eucalyptus camaldulensis (Ec) and two shallow-rooted willow clones: Salix matsudana x Salix alba (SmxSa) and Salix nigra (Sn4). Individuals of the three taxa were grown in pots and assigned to either of four treatments: Control (well-watered plants), well-watered followed by drought (C + D); waterlogged for 15 days followed by drought (W15d + D) and waterlogged for 30 days followed by drought (W30d + D). Biomass allocation, growth (diameter, height, length of leaves, and roots), specific leaf area, stomatal conductance, water potential, hydraulic conductivity of roots and branches, leaf C13 and root cortical aerenchyma formation were determined at different stages of the experiment. Ec growth was not affected by W + D, developing tolerance strategies at leaf and whole plant levels. Differential effects of W + D were observed in both Salix clones depending on the time of waterlogging. In Sn4 and SmxSa, the root biomass was affected in W15d + D treatment, but a root tolerance response (aerenchyma and adventitious root formation) was observed in W30d + D. In the three taxa, and contrary to expectations, the previous exposure to a waterlogging period did not increase the susceptibility of the plants to a subsequent drought event. On the contrary, we found tolerance, which depended on the time of waterlogging exposure.

Comparative Physiological and Transcriptome Analysis Reveals Potential Pathways and Specific Genes Involved in Waterlogging Tolerance in Apple Rootstocks

Apple (Malus × domestica Borkh.) is one of the most cultivated fruit crops in China. Apple trees frequently encounter waterlogging stress, mainly due to excess rainfall, soil compaction, or poor soil drainage, results in yellowing leaves and declined fruit quality and yield in some regions. However, the mechanism underlying the response to waterlogging has not been well elucidated. Therefore, we performed a physiological and transcriptomic analysis to examine the differential responses of two apple rootstocks (waterlogging-tolerant M. hupehensis and waterlogging-sensitive M. toringoides) to waterlogging stress. The results showed that M. toringoides displayed more severe leaf chlorosis during the waterlogging treatment than M. hupehensis. Compared with M. hupehensis, the more severe leaf chlorosis induced by waterlogging stress in M. toringoides was highly correlated with increased electrolyte leakage and superoxide radicals, hydrogen peroxide accumulation, and increased stomata closure. Interestingly, M. toringoides also conveyed a higher ethylene production under waterlogging stress. Furthermore, RNA-seq revealed that a total of 13,913 common differentially expressed genes (DEGs) were differentially regulated between M. hupehensis and M. toringoides under waterlogging stress, especially those DEGs involved in the biosynthesis of flavonoids and hormone signaling. This suggests a possible link of flavonoids and hormone signaling to waterlogging tolerance. Taken together, our data provide the targeted genes for further investigation of the functions, as well as for future molecular breeding of waterlogging-tolerant apple rootstocks.

Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants

Mulberry (Morus alba), a widely distributed economic plant, can withstand long-term flooding stress. However, the regulatory gene network underlying this tolerance is unknown. In the present study, mulberry plants were subjected to submergence stress. Subsequently, mulberry leaves were collected to perform quantitative reverse-transcription PCR (qRT-PCR) and transcriptome analysis. Genes encoding ascorbate peroxidase and glutathione S-transferase were significantly upregulated after submergence stress, indicating that they could protect the mulberry plant from flood damage by mediating ROS homeostasis. Genes that regulate starch and sucrose metabolism; genes encoding pyruvate kinase, alcohol dehydrogenase, and pyruvate decarboxylase (enzymes involved in glycolysis and ethanol fermentation); and genes encoding malate dehydrogenase and ATPase (enzymes involved in the TCA cycle) were also obviously upregulated. Hence, these genes likely played a key role in mitigating energy shortage during flooding stress. In addition, genes associated with ethylene, cytokinin, abscisic acid, and MAPK signaling; genes involved in phenylpropanoid biosynthesis; and transcription factor genes also showed upregulation under flooding stress in mulberry plants. These results provide further insights into the adaptation mechanisms and genetics of submergence tolerance in mulberry plants and could aid in the molecular breeding of these plants.

Ethylene and Jasmonates Signaling Network Mediating Secondary Metabolites under Abiotic Stress

Plants are sessile organisms that face environmental threats throughout their life cycle, but increasing global warming poses an even more existential threat. Despite these unfavorable circumstances, plants try to adapt by developing a variety of strategies coordinated by plant hormones, resulting in a stress-specific phenotype. In this context, ethylene and jasmonates (JAs) present a fascinating case of synergism and antagonism. Here, Ethylene Insensitive 3/Ethylene Insensitive-Like Protein1 (EIN3/EIL1) and Jasmonate-Zim Domain (JAZs)-MYC2 of the ethylene and JAs signaling pathways, respectively, appear to act as nodes connecting multiple networks to regulate stress responses, including secondary metabolites. Secondary metabolites are multifunctional organic compounds that play crucial roles in stress acclimation of plants. Plants that exhibit high plasticity in their secondary metabolism, which allows them to generate near-infinite chemical diversity through structural and chemical modifications, are likely to have a selective and adaptive advantage, especially in the face of climate change challenges. In contrast, domestication of crop plants has resulted in change or even loss in diversity of phytochemicals, making them significantly more vulnerable to environmental stresses over time. For this reason, there is a need to advance our understanding of the underlying mechanisms by which plant hormones and secondary metabolites respond to abiotic stress. This knowledge may help to improve the adaptability and resilience of plants to changing climatic conditions without compromising yield and productivity. Our aim in this review was to provide a detailed overview of abiotic stress responses mediated by ethylene and JAs and their impact on secondary metabolites.

Physiological, biochemical, and metabolic changes in diploid and triploid watermelon leaves during flooding

Background

Flooding is a major stress factor impacting watermelon growth and production globally. Metabolites play a crucial role in coping with both biotic and abiotic stresses.

Methods

In this study, diploid (2X) and triploid (3X) watermelons were investigated to determine their flooding tolerance mechanisms by examining physiological, biochemical, and metabolic changes at different stages. Metabolite quantification was done using UPLC-ESI-MS/MS and a total of 682 metabolites were detected.

Results

The results showed that 2X watermelon leaves had lower chlorophyll content and fresh weights compared to 3X. The activities of antioxidants, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were higher in 3X than in 2X. 3X watermelon leaves showed lower O2 production rates, MDA, and hydrogen peroxide (H2O2) levels in response to flooding, while higher ethylene production was observed. 3X had higher levels of dehydrogenase activity (DHA) and ascorbic acid + dehydrogenase (AsA + DHA), but both 2X and 3X showed a significant decline in the AsA/DHA ratio at later stages of flooding. Among them, 4-guanidinobutyric acid (mws0567), an organic acid, may be a candidate metabolite responsible for flooding tolerance in watermelon and had higher expression levels in 3X watermelon, suggesting that triploid watermelon is more tolerant to flooding.

Conclusion

This study provides insights into the response of 2X and 3X watermelon to flooding and the physiological, biochemical, and metabolic changes involved. It will serve as a foundation for future in-depth molecular and genetic studies on flooding response in watermelon.

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.

Submergence promotes auxin-induced callus formation through ethylene-mediated post-transcriptional control of auxin receptors

Plant cells in damaged tissue can be reprogrammed to acquire pluripotency and induce callus formation. However, in the aboveground organs of many species, somatic cells that are distal to the wound site become less sensitive to auxin-induced callus formation, suggesting the existence of repressive regulatory mechanisms that are largely unknown. Here we reveal that submergence-induced ethylene signals promote callus formation by releasing post-transcriptional silencing of auxin receptor transcripts in non-wounded regions. We determined that short-term submergence of intact seedlings induces auxin-mediated cell dedifferentiation across the entirety of Arabidopsis thaliana explants. The constitutive triple response 1-1 (ctr1-1) mutation induced callus formation in explants without submergence, suggesting that ethylene facilitates cell dedifferentiation. We show that ETHYLENE-INSENSITIVE 2 (EIN2) post-transcriptionally regulates the abundance of transcripts for auxin receptor genes by facilitating microRNA393 degradation. Submergence-induced calli in non-wounded regions were suitable for shoot regeneration, similar to those near the wound site. We also observed submergence-promoted callus formation in Chinese cabbage (Brassica rapa), indicating that this may be a conserved mechanism in other species. Our study identifies previously unknown regulatory mechanisms by which ethylene promotes cell dedifferentiation and provides a new approach for boosting callus induction efficiency in shoot explants.

Foliar Application of Spermidine Alleviates Waterlogging-Induced Damages to Maize Seedlings by Enhancing Antioxidative Capacity, Modulating Polyamines and Ethylene Biosynthesis

Waterlogging is a major threat to maize production worldwide. The exogenous application of spermidine is well known to enhance plant tolerance to abiotic stresses. The role of exogenous spermidine application in waterlogging tolerance in maize was investigated in this study. Two maize varieties (a waterlogging-tolerant variety: Xundan 20 (XD20) and a waterlogging-sensitive variety: Denghai 662 (DH662)) were subjected to waterlogging stress at the seedling stage, and then foliar spraying of 0.75 mM spermidine or purified water. Findings demonstrated lower chlorophyll content, reduced growth indices, considerable increase in superoxide anion (O2-) generation rate, and H2O2/malondialdehyde accumulation in the two maize varieties under waterlogging stress compared to the control treatment. However, the tolerance variety performed better than the sensitive one. Foliar application of spermidine significantly increased antioxidant enzyme activities under waterlogging stress. In addition, the application of spermidine increased polyamine levels and led to the reduction of ethylene levels under waterlogging. Consequences of spermidine application were most apparent for the waterlogging-sensitive cultivar DH662 under waterlogging than the waterlogging-tolerant variety XD20.

Ecological strategy of Phyllostachys heteroclada oliver in the riparian zone based on ecological stoichiometry

The abnormality of seasonal water level fluctuation in the riparian zone causes various ecological and environmental problems, such as vegetation degradation, biodiversity reduction, soil erosion, and landscape transformation, thereby critically modifying the ecosystem structure and functions. This necessitates the development of a dominant vegetation zone with competitive potential. In this study, we investigated the content and distribution pattern of nutrient elements in each organ of the dominant bamboo species, Phyllostachys heteroclada, in the riparian zone. We also analyzed the morphological characteristics, root aeration tissue structure, root oxygen exchange capacity, ATP supply situation, and leaf PSII photosynthetic mechanism of two bamboo species (P. heteroclada and P. nigra) in the riparian zone. Compared with P. nigra, the roots of P. heteroclada formed well-developed oxygen storage and transport structure, i.e., aeration tissue, and exhibited root oxygen secretion in the waterlogging environment of the riparian zone, whereas the roots maintained a high ATP content through energy metabolism, thus benefiting mineral absorption and transport. Moreover, the accumulation of N, P, Ca, Mg, and Fe in the leaves of P. heteroclada was greater under waterlogging conditions than under non-waterlogging conditions, which is the basis for the efficient operation of the photosynthetic mechanism of the leaves. Compared with waterlogged P. nigra, the PSII electron acceptor Q_A of P. heteroclada leaves had a vigorous reducing ability and showed higher efficiency of light uptake energy as well as higher quantum yield indexes ϕ(Eo) and ϕ(Po). This study demonstrates that the ecological adaptive regulation strategies of P. heteroclada in the riparian zone are intrinsic driving factors affecting their stoichiometric characteristics, including changes in the absorption and transport of minerals caused by root aeration structure and energy metabolism. Moreover, carbon production and allocation may be caused by the stable photosynthetic mechanism and source-sink relationship of leaves. Through the synergistic regulation of different organs realizing their roles and functions, P. heteroclada developed ecological stoichiometry characteristics adapted to the riparian zone.

Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.

The Role of Aquaporins in Plant Growth under Conditions of Oxygen Deficiency

Plants frequently experience hypoxia due to flooding caused by intensive rainfall or irrigation, when they are partially or completely submerged under a layer of water. In the latter case, some resistant plants implement a hypoxia avoidance strategy by accelerating shoot elongation, which allows lifting their leaves above the water surface. This strategy is achieved due to increased water uptake by shoot cells through water channels (aquaporins, AQPs). It remains a puzzle how an increased flow of water through aquaporins into the cells of submerged shoots can be achieved, while it is well known that hypoxia inhibits the activity of aquaporins. In this review, we summarize the literature data on the mechanisms that are likely to compensate for the decline in aquaporin activity under hypoxic conditions, providing increased water entry into cells and accelerated shoot elongation. These mechanisms include changes in the expression of genes encoding aquaporins, as well as processes that occur at the post-transcriptional level. We also discuss the involvement of hormones, whose concentration changes in submerged plants, in the control of aquaporin activity.

High-throughput unmanned aerial vehicle-based phenotyping provides insights into the dynamic process and genetic basis of rapeseed waterlogging response in the field

Waterlogging severely affects the growth, development, and yield of crops. Accurate high-throughput phenotyping is important for exploring the dynamic crop waterlogging response in the field, and the genetic basis of waterlogging tolerance. In this study, a multi-model remote sensing phenotyping platform based on an unmanned aerial vehicle (UAV) was used to assess the genetic response of rapeseed (Brassica napus) to waterlogging, by measuring morphological traits and spectral indices over 2 years. The dynamic responses of the morphological and spectral traits indicated that the rapeseed waterlogging response was severe before the middle stage within 18 d after recovery, but it subsequently decreased partly. Genome-wide association studies identified 289 and 333 loci associated with waterlogging tolerance in 2 years. Next, 25 loci with at least nine associations with waterlogging-related traits were defined as highly reliable loci, and 13 loci were simultaneously identified by waterlogging tolerance coefficients of morphological traits, spectral indices, and common factors. Forty candidate genes were predicted in the regions of 13 overlapping loci. Our study provides insights into the understanding of the dynamic process and genetic basis of rapeseed waterlogging response in the field by a high-throughput UAV phenotyping platform. The highly reliable loci identified in this study are valuable for breeding waterlogging-tolerant rapeseed cultivars.

Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

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.