Rapid flooding-induced adventitious root development from preformed primordia in Solanum dulcamara

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.

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.

Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings

MAIN CONCLUSION

Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.

A CsEIL3-CsARN6.1 module promotes waterlogging-triggered adventitious root formation in cucumber by activating the expression of CsPrx5

The formation of adventitious roots (ARs) derived from hypocotyl is the most important morphological adaptation to waterlogging stress in Cucumis sativus (cucumber). Our previous study showed that cucumbers with the gene CsARN6.1, encoding an AAA ATPase domain-containing protein, were more tolerant to waterlogging through increased AR formation. However, the apparent function of CsARN6.1 remained unknown. Here, we showed that the CsARN6.1 signal was predominantly observed throughout the cambium of hypocotyls, where de novo AR primordia are formed upon waterlogging treatment. The silencing of CsARN6.1 expression by virus-induced gene silencing and CRISPR/Cas9 technologies adversely affects the formation of ARs under conditions of waterlogging. Waterlogging treatment significantly induced ethylene production, thus upregulating CsEIL3 expression, which encodes a putative transcription factor involved in ethylene signaling. Furthermore, yeast one-hybrid, electrophoretic mobility assay and transient expression analyses showed that CsEIL3 binds directly to the CsARN6.1 promoter to initiate its expression. CsARN6.1 was found to interact with CsPrx5, a waterlogging-responsive class-III peroxidase that enhanced H₂ O₂ production and increased AR formation. These data provide insights into understanding the molecular mechanisms of AAA ATPase domain-containing protein and uncover a molecular mechanism that links ethylene signaling with the formation of ARs triggered by waterlogging.

Plant–Microbe Interactions under the Action of Heavy Metals and under the Conditions of Flooding

Heavy metals and flooding are among the primary environmental factors affecting plants and microorganisms. This review separately considers the impact of heavy metal contamination of soils on microorganisms and plants, on plant and microbial biodiversity, and on plant–microorganism interactions. The use of beneficial microorganisms is considered one of the most promising methods of increasing stress tolerance since plant-associated microbes reduce metal accumulation, so the review focuses on plant–microorganism interactions and their practical application in phytoremediation. The impact of flooding as an adverse environmental factor is outlined. It has been shown that plants and bacteria under flooding conditions primarily suffer from a lack of oxygen and activation of anaerobic microflora. The combined effects of heavy metals and flooding on microorganisms and plants are also discussed. In conclusion, we summarize the combined effects of heavy metals and flooding on microorganisms and plants.

Steroidal glycoside profile differences among primary roots system and adventitious roots in Solanum dulcamara

Solanum dulcamara primary and adventitious roots showed qualitative and quantitative differences in their steroidal glycosides profile. This opened new venues to evaluate the bioactivity of these molecules in belowground ecosystems. The Solanum genus is characterized by the presence of steroidal glycosides (SGs) that confer herbivore resistance and serve as drug precursors in the pharmaceutical industry. Solanum dulcamara is a self-compatible, sexually reproducing species that produces seeds after buzz-pollination. In addition, primordia on the stem facilitate clonal propagation via adventitious root (AR) formation. ARs contain aerenchyma being developmentally and morphologically different from primary roots (PRs). Therefore, we hypothesized that ARs and PRs have different SG profiles. Aiming to assess differences in SGs profiles in S. dulcamara roots in relation to their origins and morphologies, we used liquid chromatography coupled to electron spray ionization quadruple time of flight mass spectrometry (LC-ESI-qToF-MS) to profile SGs from PRs and ARs of seven S. dulcamara individuals. Mass fragmentation pattern analysis indicated the presence of 31 SG-type structures, including those with spirostans and furostans moieties. We assigned the 31 structures to 9 classes of steroidal aglycons (SAgls) that differ in hydroxylation and degree of unsaturation. We found that SAgls were conjugated with di-, tri- and tetra saccharides whereby one compound contained a malonylated sugar. Principle component analysis showed that SG profiles of PRs and ARs separated on the first principal component, supporting our hypothesis. Specifically, PRs contain higher number of SGs than ARs with some compounds exclusively present in PRs. Our results reveal a high level of novel chemodiversity in PRs and ARs of Solanum dulcamara. The knowledge gained will deepen our understanding of SGs biosynthesis and their functional role in plant-environment interactions.

Volatile organic compounds shape belowground plant-fungi interactions

Volatile organic compounds (VOCs), a bouquet of chemical compounds released by all life forms, play essential roles in trophic interactions. VOCs can facilitate a large number of interactions with different organisms belowground. VOCs-regulated plant-plant or plant-insect interaction both below and aboveground has been reported extensively. Nevertheless, there is little information about the role of VOCs derived from soilborne pathogenic fungi and beneficial fungi, particularly mycorrhizae, in influencing plant performance. In this review, we show how plant VOCs regulate plant-soilborne pathogenic fungi and beneficial fungi (mycorrhizae) interactions. How fungal VOCs mediate plant-soilborne pathogenic and beneficial fungi interactions are presented and the most common methods to collect and analyze belowground volatiles are evaluated. Furthermore, we suggest a promising method for future research on belowground VOCs.

RNA-Seq Reveals Waterlogging-Triggered Root Plasticity in Mungbean Associated with Ethylene and Jasmonic Acid Signal Integrators for Root Regeneration

Global climate changes increase the frequency and intensity of heavy precipitation events, which result in flooding or soil waterlogging. One way to overcome these low-oxygen stresses is via modifying the plant root system to improve internal aeration. Here, we used a comparative RNA-seq based transcriptomic approach to elucidate the molecular mechanisms of waterlogging-triggered root plasticity in mungbean (Vigna radiata), a major grain legume cultivated in Asia. Two mungbean varieties with contrasting waterlogging tolerance due to the plasticity of the root system architecture were subjected to short-term and long-term waterlogging. Then, RNA-seq was performed. Genes highly expressed in both genotypes under short-term waterlogging are related to glycolysis and fermentation. Under long-term waterlogging, the expression of these genes was less induced in the tolerant variety, suggesting it had effectively adapted to waterlogging via enhancing root plasticity. Remarkably, under short-term waterlogging, the expression of several transcription factors that serve as integrators for ethylene and jasmonic acid signals controlling root stem cell development was highly upregulated only in the tolerant variety. Sequentially, root development-related genes were more expressed in the tolerant variety under long-term waterlogging. Our findings suggest that ethylene and jasmonic acids may contribute to waterlogging-triggered root plasticity by relaying environmental signals to reprogram root regeneration. This research provides the basis for the breeding and genetic engineering of waterlogging-tolerant crops in the future.

Belowground plant-microbe communications via volatile compounds

Volatile compounds play important roles in rhizosphere biological communications and interactions. The emission of plant and microbial volatiles is a dynamic phenomenon that is affected by several endogenous and exogenous signals. Diffusion of volatiles can be limited by their adsorption, degradation, and dissolution under specific environmental conditions. Therefore, rhizosphere volatiles need to be investigated on a micro and spatiotemporal scale. Plant and microbial volatiles can expand and specialize the rhizobacterial niche not only by improving the root system architecture such that it serves as a nutrient-rich shelter, but also by inhibiting or promoting the growth, chemotaxis, survival, and robustness of neighboring organisms. Root volatiles play an important role in engineering the belowground microbiome by shaping the microbial community structure and recruiting beneficial microbes. Microbial volatiles are appropriate candidates for improving plant growth and health during environmental challenges and climate change. However, some technical and experimental challenges limit the non-destructive monitoring of volatile emissions in the rhizosphere in real-time. In this review, we attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.

Adventitious root primordia formation and development in the stem of Ananas comosus var. bracteatus slip

There are about 4-6 slips on a fruit, and they are good materials for effective regeneration of Ananas comosus var. bracteatus. Adventitious root (AR) induction is essential for the propagation of Ananas comosus var. bracteatus slips. Growth regulator treatment, and culture medium are imperative factors that affect slip growth and rooting. In order to screen the optimal methods for slips rooting and reveal the anatomic procedure of slip rooting, this study induced slip rooting by different treatment of growth regulator, culture medium, observed the slip stem structure, AR origination and formation procedure through paraffin sections. The results showed that, slip cuttings treated with 100 mg/L of Aminobenzotriazole (ABT) for 6 hrs, cultured in river sand: coconut chaff: garden soil 2:2:1 medium is the optimal method for rooting. The proper supplementary of ABT can enhance the soluble sugar content, soluble protein content, polyphenol oxidase (PPO) activity and peroxidase (POD) enzyme activity, which resulted in the improvement of rooting. The slip stem structure is quite different from other monocots, which consists of epidermis, cortex, and stele with vascular tissues distributed in the cortex and stele. The AR primordia originates from the parenchyma cells located on the borderline between the cortex and stele. The vascular tissues in the AR develop and are connected with vascular tissue of the stem before the AR grew out the stem. The number of primary xylem poles in AR is about 30.

Response of Mungbean (cvs. Celera II-AU and Jade-AU) and Blackgram (cv. Onyx-AU) to Transient Waterlogging

Mungbean [Vigna radiata (L.) Wilczek] and blackgram [Vigna mungo (L.) Hepper] are important crops for smallholder farmers in tropical and subtropical regions. Production of both crops is affected by unexpected and increasingly frequent extreme precipitation events, which result in transient soil waterlogging. This study aimed to compare the waterlogging tolerance of mungbean and blackgram genotypes under the varying duration of waterlogging stress at germination and seedling stages. We evaluated the responses to different durations of transient waterlogging in a sandy clay loam under temperature-controlled glasshouse conditions. Waterlogging durations were 0, 1, 2, 3, 4, 5, 6, 7, and 8 days during germination and 0, 2, 4, 8, and 16 days during the seedling stage. We used two mungbean genotypes (green testa), Celera II-AU (small-seeded), and Jade-AU (large-seeded), contrasting in seed size and hypocotyl pigmentation, and a blackgram genotype (black testa), Onyx-AU. Waterlogging reduced soil redox potential, delayed or even prevented germination, decreased seedling establishment, and affected shoot and root development. In the seedlings waterlogged (WL) at 15 days after sowing (DAS), adventitious root formation and crown nodulation varied between the genotypes, and 16 days of waterlogging substantially reduced growth but did not result in plant death. Plants in soil with waterlogging for 8-16 days followed by drainage and sampling at 39 DAS had reduced shoot and root dry mass by 60-65% in mungbean and 40% in blackgram compared with continuously drained controls, due at least in part to fewer lateral roots. Soil plant analysis development (SPAD) chlorophyll content was also reduced. Onyx-AU, a blackgram genotype, was more tolerant to transient waterlogging than Jade-AU and Celera II-AU in both growth stages. Of the two mungbean genotypes, Celera II-AU had a greater seedling establishment than Jade-AU post waterlogging imposed at sowing. In contrast, Jade-AU had more plant biomass and greater recovery growth than Celera II-AU after waterlogging and recovery during the seedling stage. Both species were delayed in emergence in response to the shorter periods of transient waterlogging at germination, and with the longer waterlogging germination and emergence failed, whereas at the seedling stage both showed adaptation by the formation of adventitious roots.

Depicting the molecular responses of adventitious rooting to waterlogging in melon hypocotyls by transcriptome profiling

Waterlogging is a severe abiotic stressor that inhibits crop growth and productivity owing to the decline in the amount of oxygen available to the waterlogged organs. Although melon (Cucumis melo L.) is sensitive to waterlogging, its ability to form adventitious roots facilitates the diffusion of oxygen and allows the plant to survive waterlogging. To provide comprehensive insight into the adventitious rooting in response to waterlogging of melon, global transcriptome changes during this process were investigated. Of the 17,146 genes expressed during waterlogging, 7363 of them were differentially expressed in the pairwise comparisons between different waterlogging treatment time points. A further analysis suggested that the genes involved in sugar cleavage, glycolysis, fermentation, reactive oxygen species scavenging, cell wall modification, cell cycle governing, microtubule remodeling, hormone signals and transcription factors could play crucial roles in the adventitious root production induced by waterlogging. Additionally, ethylene and ERFs were found to be vital factors that function in melon during adventitious rooting. This study broadens our understanding of the mechanisms that underlie adventitious rooting induced by waterlogging and lays the theoretical foundation for further molecular breeding of waterlogging-tolerant melon.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02866-w.

An auxin-mediated regulatory framework for wound-induced adventitious root formation in tomato shoot explants

Adventitious roots (ARs) are produced from non-root tissues in response to different environmental signals, such as abiotic stresses, or after wounding, in a complex developmental process that requires hormonal crosstalk. Here, we characterized AR formation in young seedlings of Solanum lycopersicum cv. 'Micro-Tom' after whole root excision by means of physiological, genetic and molecular approaches. We found that a regulated basipetal auxin transport from the shoot and local auxin biosynthesis triggered by wounding are both required for the re-establishment of internal auxin gradients within the vasculature. This promotes cell proliferation at the distal cambium near the wound in well-defined positions of the basal hypocotyl and during a narrow developmental window. In addition, a pre-established pattern of differential auxin responses along the apical-basal axis of the hypocotyl and an as of yet unknown cell-autonomous inhibitory pathway contribute to the temporal and spatial patterning of the newly formed ARs on isolated hypocotyl explants. Our work provides an experimental outline for the dissection of wound-induced AR formation in tomato, a species that is suitable for molecular identification of gene regulatory networks via forward and reverse genetics approaches.

Plant Morphological, Physiological and Anatomical Adaption to Flooding Stress and the Underlying Molecular Mechanisms

Globally, flooding is a major threat causing substantial yield decline of cereal crops, and is expected to be even more serious in many parts of the world due to climatic anomaly in the future. Understanding the mechanisms of plants coping with unanticipated flooding will be crucial for developing new flooding-tolerance crop varieties. Here we describe survival strategies of plants adaptation to flooding stress at the morphological, physiological and anatomical scale systemically, such as the formation of adventitious roots (ARs), aerenchyma and radial O₂ loss (ROL) barriers. Then molecular mechanisms underlying the adaptive strategies are summarized, and more than thirty identified functional genes or proteins associated with flooding-tolerance are searched out and expounded. Moreover, we elaborated the regulatory roles of phytohormones in plant against flooding stress, especially ethylene and its relevant transcription factors from the group VII Ethylene Response Factor (ERF-VII) family. ERF-VIIs of main crops and several reported ERF-VIIs involving plant tolerance to flooding stress were collected and analyzed according to sequence similarity, which can provide references for screening flooding-tolerant genes more precisely. Finally, the potential research directions in the future were summarized and discussed. Through this review, we aim to provide references for the studies of plant acclimation to flooding stress and breeding new flooding-resistant crops in the future.

Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?

Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.

Ethylene Differentially Modulates Hypoxia Responses and Tolerance across Solanum Species

The increasing occurrence of floods hinders agricultural crop production and threatens global food security. The majority of vegetable crops are highly sensitive to flooding and it is unclear how these plants use flooding signals to acclimate to impending oxygen deprivation (hypoxia). Previous research has shown that the early flooding signal ethylene augments hypoxia responses and improves survival in Arabidopsis. To unravel how cultivated and wild Solanum species integrate ethylene signaling to control subsequent hypoxia acclimation, we studied the transcript levels of a selection of marker genes, whose upregulation is indicative of ethylene-mediated hypoxia acclimation in Arabidopsis. Our results suggest that ethylene-mediated hypoxia acclimation is conserved in both shoots and roots of the wild Solanum species bittersweet (Solanum dulcamara) and a waterlogging-tolerant potato (Solanum tuberosum) cultivar. However, ethylene did not enhance the transcriptional hypoxia response in roots of a waterlogging-sensitive potato cultivar, suggesting that waterlogging tolerance in potato could depend on ethylene-controlled hypoxia responses in the roots. Finally, we show that ethylene rarely enhances hypoxia-adaptive genes and does not improve hypoxia survival in tomato (Solanum lycopersicum). We conclude that analyzing genes indicative of ethylene-mediated hypoxia acclimation is a promising approach to identifying key signaling cascades that confer flooding tolerance in crops.

The Many Facets of Hypoxia in Plants

Plants are aerobic organisms that require oxygen for their respiration. Hypoxia arises due to the insufficient availability of oxygen, and is sensed by plants, which adapt their growth and metabolism accordingly. Plant hypoxia can occur as a result of excessive rain and soil waterlogging, thus constraining plant growth. Increasing research on hypoxia has led to the discovery of the mechanisms that enable rice to be productive even when partly submerged. The identification of Ethylene Response Factors (ERFs) as the transcription factors that enable rice to survive submergence has paved the way to the discovery of oxygen sensing in plants. This, in turn has extended the study of hypoxia to plant development and plant–microbe interaction. In this review, we highlight the many facets of plant hypoxia, encompassing stress physiology, developmental biology and plant pathology.

Tolerant mechanisms to O2 deficiency under submergence conditions in plants

Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.

Small RNA sequencing identifies cucumber miRNA roles in waterlogging-triggered adventitious root primordia formation

The formation of adventitious roots (ARs) is a key morphological adaptation of cucumber (Cucumis sativus L.) to waterlogging stress. MicroRNAs (miRNAs) constitute a group of non-coding small RNAs (sRNA) that play crucial roles in regulating diverse biological processes, including waterlogging acclimation. However, which specific miRNAs and how they are involved in waterlogging-triggered de novo AR primordia formation are not fully known. Here, Illumina sRNA sequencing was applied to sequence six sRNA libraries generated from the waterlogging-tolerant cucumber Zaoer-N after 48 h of waterlogging and the control. A total of 358 cucumber miRNAs, 312 known and 46 novel, were obtained. Among them, 23 were differentially expressed, with 10 and 13 being up- and downregulated, respectively. A qPCR expression study confirmed that the identified differentially expressed miRNAs were credible. A total of 657 putative miRNA target genes were predicted for the 23 miRNAs using an in silico approach. A gene ontology enrichment analysis revealed that target genes functioning in cell redox homeostasis, cytoskeleton, photosynthesis and cell growth were over-represented. In total, 58 of the 657 target genes showed inverse expression patterns compared with their respective miRNAs through a combined analysis of sRNA- and RNA-sequencing-based transcriptome datasets using the same experimental design. The target gene annotation included a peroxidase, a GDSL esterases/lipase and two heavy metal-associated isoprenylated plant proteins. Our results provide an important framework for understanding the unique miRNA patterns seen in responses to waterlogging and the miRNA-mediated formation of de novo AR primordia in cucumber.

Flooding with shallow water promotes the invasiveness of Mikania micrantha

The invasive ability of alien plants is not only affected by their biological characteristics but also by environmental factors. Therefore, investigating the relationship between plant growth and environmental factors is helpful for predicting the invasive potential of alien species. Mikania micrantha H.B.K. (a vine of Asteraceae) is one of the top 10 most invasive weeds worldwide and causes serious damage to agroforestry ecosystems. Water is an important environmental factor that affects plant growth; however, the relationship between water conditions and the rapid growth of M. micrantha is not clear. In this study, 162 M. micrantha population sizes were investigated in dry, wet and aquatic habitats in the Pearl River Delta region of Guangdong, China. In addition, the seed germination and seedling growth characteristics of M. micrantha were determined by submerging tests. The results showed that the population size of M. micrantha was the largest in aquatic habitats, and the soil moisture content was positively correlated to the population size in dry and wet habitats. Furthermore, M. micrantha seeds could germinate underwater and grow out of the water surface at a depth of 6 cm with a survival rate of 7.4%. Aquatic habitat promoted vine elongation, whereas dry habitats resulted in the reverse pattern. After 8 weeks of water treatments, the vine stem length was 2 and 3 times longer in the aquatic habitat than the wet and dry habitats, respectively. The total root length, root volume, and root tip number increased significantly in the aquatic habitat when compared to those in the wet habitat; however, these parameters exhibited the opposite pattern in the dry habitat. The results showed that flooding with shallow water is conducive to the invasiveness of M. micrantha, suggesting that water is the key determinant during the intrusion process of M. micrantha populations.

OPEN RESEARCH BADGES

This article has been awarded Open Data, Open Materials and Preregistered research design Badges. All materials and data are publicly accessible via the Open Science Framework at https://osf.io/ksz2f/?viewonly=30b6fec21f0447edbdfc9cebe2b01065, https://osf.io/a5ymf/ and https://osf.io/ksz2fl?viewonly=cfcbfOfc829c402fb22deb3be801dffc.

What Makes Adventitious Roots?

The spermatophyte root system is composed of a primary root that develops from an embryonically formed root meristem, and of different post-embryonic root types: lateral and adventitious roots. Adventitious roots, arising from the stem of the plants, are the main component of the mature root system of many plants. Their development can also be induced in response to adverse environmental conditions or stresses. Here, in this review, we report on the morphological and functional diversity of adventitious roots and their origin. The hormonal and molecular regulation of the constitutive and inducible adventitious root initiation and development is discussed. Recent data confirmed the crucial role of the auxin/cytokinin balance in adventitious rooting. Nevertheless, other hormones must be considered. At the genetic level, adventitious root formation integrates the transduction of external signals, as well as a core auxin-regulated developmental pathway that is shared with lateral root formation. The knowledge acquired from adventitious root development opens new perspectives to improve micropropagation by cutting in recalcitrant species, root system architecture of crops such as cereals, and to understand how plants adapted during evolution to the terrestrial environment by producing different post-embryonic root types.

Endogenous Hypoxia in Lateral Root Primordia Controls Root Architecture by Antagonizing Auxin Signaling in Arabidopsis

As non-photosynthesizing organs, roots are dependent on diffusion of oxygen from the external environment and, in some instances, from the shoot for their aerobic metabolism. Establishment of hypoxic niches in the developing tissues of plants has been postulated as a consequence of insufficient diffusion of oxygen to satisfy the demands throughout development. Here, we report that such niches are established at specific stages of lateral root primordia development in Arabidopsis thaliana grown under aerobic conditions. Using gain- and loss-of-function mutants, we show that ERF-VII transcription factors, which mediate hypoxic responses, control root architecture by acting in cells with a high level of auxin signaling. ERF-VIIs repress the expression of the auxin-induced genes LBD16, LBD18, and PUCHI, which are essential for lateral root development, by binding to their promoters. Our results support a model in which the establishment of hypoxic niches in the developing lateral root primordia contributes to the shutting down of key auxin-induced genes and regulates the production of lateral roots.

Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation in Arabidopsis

Soil water-logging and flooding are common environmental stress conditions that can impair plant fitness. Roots are the first organs to be confronted with reduced oxygen tension as a result of flooding. While anatomical and morphological adaptations of roots are extensively studied, the root system architecture is only now becoming a focus of flooding research. Adventitious root (AR) formation shifts the root system higher up the plant, thereby facilitating supply with oxygen, and thus improving root and plant survival. We used Arabidopsis knockout mutants and overexpressors of ERFVII transcription factors to study their role in AR formation under hypoxic conditions and in response to ethylene. Results show that ethylene inhibits AR formation. Hypoxia mainly promotes AR elongation rather than formation mediated by ERFVII transcription factors, as indicated by reduced AR elongation in erfVII seedlings. Overexpression of HRE2 induces AR elongation to the same degree as hypoxia, while ethylene overrides HRE2-induced AR elongation. The ERFVII transcription factors promote establishment of an AR system that is under negative control by ethylene. Inhibition of growth of the main root system and promotion of AR elongation under hypoxia strengthens the root system in upper soil layers where oxygen shortage may last for shorter time periods.

A proteomics analysis of adventitious root formation after leaf removal in lotus (Nelumbo nucifera Gaertn.)

The formation of adventitious roots (ARs) is an important process for lotus (Nelumbo nucifera), which does not have a well-formed main root. In lotus, the removal of leaves above the waterline significantly promoted AR formation, while the removal of leaves below the waterline inhibited AR formation. Proteins were identified using isobaric tags for relative and absolute quantization technique. The number of proteins decreased with increasing sequencing coverage, and most of the identified proteins had fewer than 10 peptides. In the A1/A0 and A2/A1 stages, 661 and 154 proteins showed increased abundance, respectively, and 498 and 111 proteins showed decreased abundance, respectively. In the B1/B0 and B2/B1 stages, 498 and 436 proteins showed increased abundance, respectively, and 358 and 348 proteins showed decreased abundance, respectively. Among the proteins showing large differences in abundance, 17 were identified as being related to AR formation. Proteins involved in the glycolytic pathway and the citrate cycle showed differences in abundance between the two types of leaf removal. The transcriptional levels of nine genes encoding relevant proteins were assessed by quantitative polymerase chain reaction. The results of this study illustrate the changes in metabolism after different types of leaf removal during AR formation in lotus.

Improving Flooding Tolerance of Crop Plants

A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.

Late Blight Resistance Screening of Major Wild Swedish Solanum Species: S. dulcamara, S. nigrum, and S. physalifolium

To understand the contribution of wild Solanum species to the epidemiology of potato late blight in Sweden, we characterized the resistance of the three putative alternative hosts: S. physalifolium, S. nigrum, and S. dulcamara to Phytophthora infestans, the causal agent of late blight. The pathogen sporulated in all 10 investigated S. physalifolium genotypes, suggesting susceptibility (S phenotype). Field-grown S. physalifolium was naturally infected but could regrow, though highly infected genotypes were smaller at the end of the season. In 75 S. nigrum genotypes, there were no symptoms (R phenotype) or a lesion restricted to the point of inoculation (R^N phenotype), indicating resistance. In 164 S. dulcamara genotypes, most resistance variability was found within sibling groups. In addition to the three resistance phenotypes (R, R^N, and S), in S. dulcamara a fourth new resistance phenotype (S^L) was identified with lesions larger than the point of inoculation but without visible sporulation of the pathogen. Quantitative PCR confirmed P. infestans growth difference in R^N, S^L, and S phenotypes. Thus, in Sweden S. physalifolium is susceptible and could be a player in epidemiology. A limited role of S. dulcamara leaves in the epidemiology of late blight was suggested, since no major symptoms have been found in the field.

Glycoalkaloid composition explains variation in slug resistance in Solanum dulcamara

In natural environments, plants have to deal with a wide range of different herbivores whose communities vary in time and space. It is believed that the chemical diversity within plant species has mainly arisen from selection pressures exerted by herbivores. So far, the effects of chemical diversity on plant resistance have mostly been assessed for arthropod herbivores. However, also gastropods, such as slugs, can cause extensive damage to plants. Here we investigate to what extent individual Solanum dulcamara plants differ in their resistance to slug herbivory and whether this variation can be explained by differences in secondary metabolites. We performed a series of preference assays using the grey field slug (Deroceras reticulatum) and S. dulcamara accessions from eight geographically distinct populations from the Netherlands. Significant and consistent variation in slug preference was found for individual accessions within and among populations. Metabolomic analyses showed that variation in steroidal glycoalkaloids (GAs) correlated with slug preference; accessions with high GA levels were consistently less damaged by slugs. One, strongly preferred, accession with particularly low GA levels contained high levels of structurally related steroidal compounds. These were conjugated with uronic acid instead of the glycoside moieties common for Solanum GAs. Our results illustrate how intraspecific variation in steroidal glycoside profiles affects resistance to slug feeding. This suggests that also slugs should be considered as important drivers in the co-evolution between plants and herbivores.

A disturbed auxin signaling affects adventitious root outgrowth in Solanum dulcamara under complete submergence

Flooding negatively affects the growth and even survival of most terrestrial plants. Upon flooding, the excess water quickly decreases the gas exchange between atmosphere and the submerged plant tissues, which leads to oxygen deficiency resulting in a plant cell energy crisis, and eventually plant death. Solanum dulcamara survives flooding by producing aerenchymatous adventitious roots (ARs) from pre-formed primordia on the stem, which replace the original flood-sensitive root system. However, we found that under complete submergence, AR outgrowth was impaired in S. dulcamara. In the present work, we tried to elucidate the mechanisms behind this phenomenon in particular the involvement of the phytohormones auxin, abscisic acid and jasmonic acid. Abscisic acid (ABA) is a negative regulator of AR outgrowth, but surprisingly the ABA content and signaling were decreased to a similar extent under both partial and complete submergence, suggesting that ABA might not be responsible for the difference in AR outgrowth. Auxin, which is necessary for AR outgrowth, was at similar concentrations in either partially or completely submerged primordia, but complete submergence resulted in a decrease of auxin signaling in the primordia. Application of 1-naphthaleneacetic acid (NAA) to completely submerged plants restored AR outgrowth, implying that auxin response in the rooting tissues of completely submerged plants was reduced. Furthermore, jasmonic acid (JA) concentrations did not differ between partial and complete submergence. To conclude, a disruption in the auxin signaling within S. dulcamara AR primordia may result in the abortion of AR outgrowth under complete submergence.

Environmental factors constraining adventitious root formation during flooding of Solanum dulcamara

Flooding is a compound stress, imposing strong limitations on plant development. The expression of adaptive traits that alleviate flooding stress may be constrained if floodwater levels are too deep. For instance, adventitious root outgrowth is typically less profound in completely submerged plants than in partially submerged plants, suggesting additional constraints in full submergence. As both oxygen and carbohydrates are typically limited resources under submergence, we tested the effects of oxygen concentration in the floodwater and carbohydrate status of the plants on flooding-induced adventitious root formation in Solanum dulcamara L. Partially submerged plants continued to form adventitious roots in low-oxygen floodwater, whereas completely submerged plants developed hardly any roots, even in floodwater with twice the ambient oxygen concentration. This suggests that contact with the atmosphere, enabling internal aeration, is much more important to optimal adventitious root formation than floodwater oxygen concentrations. If plants were depleted of carbohydrates before flooding, adventitious root formation in partial submergence was poor, unless high light was provided. Thus, either stored or newly produced carbohydrates can fuel adventitious root formation. These results imply that the impact of an environmental stress factor like flooding on plant performance may strongly depend on the interplay with other environmental factors.

Root Bending Is Antagonistically Affected by Hypoxia and ERF-Mediated Transcription via Auxin Signaling

When plants encounter soil water logging or flooding, roots are the first organs to be confronted with reduced gas diffusion resulting in limited oxygen supply. Since roots do not generate photosynthetic oxygen, they are rapidly faced with oxygen shortage rendering roots particularly prone to damage. While metabolic adaptations to low oxygen conditions, which ensure basic energy supply, have been well characterized, adaptation of root growth and development have received less attention. In this study, we show that hypoxic conditions cause the primary root to grow sidewise in a low oxygen environment, possibly to escape soil patches with reduced oxygen availability. This growth behavior is reversible in that gravitropic growth resumes when seedlings are returned to normoxic conditions. Hypoxic root bending is inhibited by the group VII ethylene response factor (ERFVII) RAP2.12, as rap2.12-1 seedlings show exaggerated primary root bending. Furthermore, overexpression of the ERFVII member HRE2 inhibits root bending, suggesting that primary root growth direction at hypoxic conditions is antagonistically regulated by hypoxia and hypoxia-activated ERFVIIs. Root bending is preceded by the establishment of an auxin gradient across the root tip as quantified with DII-VENUS and is synergistically enhanced by hypoxia and the auxin transport inhibitor naphthylphthalamic acid. The protein abundance of the auxin efflux carrier PIN2 is reduced at hypoxic conditions, a response that is suppressed by RAP2.12 overexpression, suggesting antagonistic control of auxin flux by hypoxia and ERFVII. Taken together, we show that hypoxia triggers an escape response of the primary root that is controlled by ERFVII activity and mediated by auxin signaling in the root tip.

Benefits of flooding-induced aquatic adventitious roots depend on the duration of submergence: linking plant performance to root functioning

Background and Aims

Temporal flooding is a common environmental stress for terrestrial plants. Aquatic adventitious roots (aquatic roots) are commonly formed in flooding-tolerant plant species and are generally assumed to be beneficial for plant growth by supporting water and nutrient uptake during partial flooding. However, the actual contribution of these roots to plant performance under flooding has hardly been quantified. As the investment into aquatic root development in terms of carbohydrates may be costly, these costs may - depending on the specific environmental conditions - offset the beneficial effects of aquatic roots. This study tested the hypothesis that the balance between potential costs and benefits depends on the duration of flooding, as the benefits are expected to outweigh the costs in long-term but not in short-term flooding.

Methods

The contribution of aquatic roots to plant performance was tested in Solanum dulcamara during 1-4 weeks of partial submergence and by experimentally manipulating root production. Nutrient uptake by aquatic roots, transpiration and photosynthesis were measured in plants differing in aquatic root development to assess the specific function of these roots.

Key Results

As predicted, flooded plants benefited from the presence of aquatic roots. The results showed that this was probably due to the contribution of roots to resource uptake. However, these beneficial effects were only present in long-term but not in short-term flooding. This relationship could be explained by the correlation between nutrient uptake and the flooding duration-dependent size of the aquatic root system.

Conclusions

The results indicate that aquatic root formation is likely to be selected for in habitats characterized by long-term flooding. This study also revealed only limited costs associated with adventitious root formation, which may explain the maintenance of the ability to produce aquatic roots in habitats characterized by very rare or short flooding events.

Transcriptomic responses of Solanum dulcamara to natural and simulated herbivory

Plants are attacked by diverse herbivores and respond with manifold defence responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet, to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds. We designed a microarray for Solanum dulcamara and showed that the transcriptional responses to real and to simulated herbivory by Spodoptera exigua overlapped moderately by about 40%. Interestingly, certain responses were mimicked better than others; 60% of the genes upregulated but not even a quarter of the genes downregulated by herbivory were similarly affected by application of oral secretions to wounds. While the regulation of genes involved in signalling, defence and water stress was mimicked well by the simulated herbivory, most of the genes related to photosynthesis, carbohydrate- and lipid metabolism were exclusively regulated by real herbivory. Thus, wounding and application of oral secretions decently mimics herbivory-induced defence responses but likely not the reallocation of primary metabolites induced by real herbivory.

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

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

The Physiology of Adventitious Roots

Adventitious roots are plant roots that form from any nonroot tissue and are produced both during normal development (crown roots on cereals and nodal roots on strawberry [Fragaria spp.]) and in response to stress conditions, such as flooding, nutrient deprivation, and wounding. They are important economically (for cuttings and food production), ecologically (environmental stress response), and for human existence (food production). To improve sustainable food production under environmentally extreme conditions, it is important to understand the adventitious root development of crops both in normal and stressed conditions. Therefore, understanding the regulation and physiology of adventitious root formation is critical for breeding programs. Recent work shows that different adventitious root types are regulated differently, and here, we propose clear definitions of these classes. We use three case studies to summarize the physiology of adventitious root development in response to flooding (case study 1), nutrient deficiency (case study 2), and wounding (case study 3).

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

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

Shade affects responses to drought and flooding - acclimation to multiple stresses in bittersweet (Solanum dulcamara L.)

Plants exposed to environmental stress often respond by a change in their phenotypic traits. These changes in trait expression may alleviate the negative effect of such stress factors. However, if multiple stresses are present, responses are likely to be less predictable and hence do not necessarily correlate to plant performance. This study tested if this expectation was true, by subjecting Solanum dulcamara plants to various simultaneous stress factors. Plants were grown in well-watered conditions, drought or flooding, and exposed to either full light or shade for 4 weeks. Shoot and root biomass, stem morphological parameters, such as height, number of nodes and length of stem internodes, and leaf traits like length, specific leaf area, chlorophyll content and stomatal conductance were determined. Both variation in light and in water availability typically caused slower growth, and resulted in distinct phenotypic changes in stem, leaf and root traits. However, effects of stresses on the expression of traits were not always additive. Instead, some combined stress responses (e.g. leaf size) appeared to be limited by physical or physiological constraints, whereas other responses were opposite to each other (e.g. root:shoot ratio), resulting in an intermediate phenotype in the combined stress treatment. These data suggest that in natural conditions, where combined stress factors are likely to be present, the optimal phenotype may not necessarily be expressed. Responses of plants to multiple stress factors may therefore not be associated with immediate advantages in terms of increased performance.

Root aeration improves growth and nitrogen accumulation in rice seedlings under low nitrogen

In wetland soils, changes in oxygen (O2) level in the rhizosphere are believed to influence the behaviour of nutrients and their usage by plants. However, the effect of aeration on nitrogen (N) acquisition under different N supply conditions remains largely unknown. In this study, the rice cultivars Yangdao 6 (YD6, with higher root aerenchyma abundance) and Nongken 57 (NK57, with lower root aerenchyma abundance) were used to evaluate the effects of aeration on rice growth and N accumulation. Our results showed that the number of adventitious roots and the root surface area increased significantly, and ethylene production and aerenchyma formation decreased in both cultivars after external aeration (EA). Five N treatments, including no N (-N), 0.125 mM NH4NO3 (LN), 1.25 mM Ca(NO3)2 (NO3-N), 1.25 mM (NH4)2SO4 (NH4-N) and 1.25 mM NH4NO3 (N/N), were applied to YD6 and NK57 for 2 days under internal aeration or EA conditions. External aeration increased the root biomass in both cultivars and the shoot biomass in NK57 by 18-50 %. The total N concentrations in roots of YD6 grown under -N and LN and of NK57 grown under NO3-N were increased by EA. Expression of OsPAD4, one of four putative genes regulating aerenchyma formation, showed a similar pattern alongside changes in the ethylene level in the EA-treated rice irrespective of the N treatments. Furthermore, expression of the high-affinity nitrate transporter gene OsNRT2.1 was increased by EA under -N, LN and NO3-N conditions. Our data provide evidence of an interaction between O2 and the supply of N in ethylene production, aerenchyma formation and N nutrition through modification of the expression of OsPAD4 and OsNRT2.1.

Ethylene-Mediated Acclimations to Flooding Stress

Flooding is detrimental for plants, primarily because of restricted gas exchange underwater, which leads to an energy and carbohydrate deficit. Impeded gas exchange also causes rapid accumulation of the volatile ethylene in all flooded plant cells. Although several internal changes in the plant can signal the flooded status, it is the pervasive and rapid accumulation of ethylene that makes it an early and reliable flooding signal. Not surprisingly, it is a major regulator of several flood-adaptive plant traits. Here, we discuss these major ethylene-mediated traits, their functional relevance, and the recent progress in identifying the molecular and signaling events underlying these traits downstream of ethylene. We also speculate on the role of ethylene in postsubmergence recovery and identify several questions for future investigations.

Life cycle stage and water depth affect flooding-induced adventitious root formation in the terrestrial species Solanum dulcamara

BACKGROUND AND AIMS

Flooding can occur at any stage of the life cycle of a plant, but often adaptive responses of plants are only studied at a single developmental stage. It may be anticipated that juvenile plants may respond differently from mature plants, as the amount of stored resources may differ and morphological changes can be constrained. Moreover, different water depths may require different strategies to cope with the flooding stress, the expression of which may also depend on developmental stage. This study investigated whether flooding-induced adventitious root formation and plant growth were affected by flooding depth in Solanum dulcamara plants at different developmental stages.

METHODS

Juvenile plants without pre-formed adventitious root primordia and mature plants with primordia were subjected to shallow flooding or deep flooding for 5 weeks. Plant growth and the timing of adventitious root formation were monitored during the flooding treatments.

KEY RESULTS

Adventitious root formation in response to shallow flooding was significantly constrained in juvenile S. dulcamara plants compared with mature plants, and was delayed by deep flooding compared with shallow flooding. Complete submergence suppressed adventitious root formation until up to 2 weeks after shoots restored contact with the atmosphere. Independent of developmental stage, a strong positive correlation was found between adventitious root formation and total biomass accumulation during shallow flooding.

CONCLUSIONS

The potential to deploy an escape strategy (i.e. adventitious root formation) may change throughout a plant's life cycle, and is largely dependent on flooding depth. Adaptive responses at a given stage of the life cycle thus do not necessarily predict how the plant responds to flooding in another growth stage. As variation in adventitious root formation also correlates with finally attained biomass, this variation may form the basis for variation in resistance to shallow flooding among plants.

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

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

Flood adaptive traits and processes: an overview

Unanticipated flooding challenges plant growth and fitness in natural and agricultural ecosystems. Here we describe mechanisms of developmental plasticity and metabolic modulation that underpin adaptive traits and acclimation responses to waterlogging of root systems and submergence of aerial tissues. This includes insights into processes that enhance ventilation of submerged organs. At the intersection between metabolism and growth, submergence survival strategies have evolved involving an ethylene-driven and gibberellin-enhanced module that regulates growth of submerged organs. Opposing regulation of this pathway is facilitated by a subgroup of ethylene-response transcription factors (ERFs), which include members that require low O₂ or low nitric oxide (NO) conditions for their stabilization. These transcription factors control genes encoding enzymes required for anaerobic metabolism as well as proteins that fine-tune their function in transcription and turnover. Other mechanisms that control metabolism and growth at seed, seedling and mature stages under flooding conditions are reviewed, as well as findings demonstrating that true endurance of submergence includes an ability to restore growth following the deluge. Finally, we highlight molecular insights obtained from natural variation of domesticated and wild species that occupy different hydrological niches, emphasizing the value of understanding natural flooding survival strategies in efforts to stabilize crop yields in flood-prone environments.