Transcriptomic Analysis of Short-Term Salt Stress Response in Watermelon Seedlings

Bacillus altitudinis AD13-4 Enhances Saline-Alkali Stress Tolerance of Alfalfa and Affects Composition of Rhizosphere Soil Microbial Community

Saline and alkaline stresses limit plant growth and reduce crop yield. Soil salinization and alkalization seriously threaten the sustainable development of agriculture and the virtuous cycle of ecology. Biofertilizers made from plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth and stress tolerance, but also are environmentally friendly and cost-effective. There have been many studies on the mechanisms underlying PGPRs enhancing plant salt resistance. However, there is limited knowledge about the interaction between PGPR and plants under alkaline-sodic stress. To clarify the mechanisms underlying PGPR's improvement of plants' tolerance to alkaline-sodic stress, we screened PGPR from the rhizosphere microorganisms of local plants growing in alkaline-sodic land and selected an efficient strain, Bacillus altitudinis AD13-4, as the research object. Our results indicate that the strain AD13-4 can produce various growth-promoting substances to regulate plant endogenous hormone levels, cell division and differentiation, photosynthesis, antioxidant capacity, etc. Transcriptome analysis revealed that the strain AD13-4 significantly affected metabolism and secondary metabolism, signal transduction, photosynthesis, redox processes, and plant-pathogen interactions. Under alkaline-sodic conditions, inoculation of the strain AD13-4 significantly improved plant biomass and the contents of metabolites (e.g., soluble proteins and sugars) as well as secondary metabolites (e.g., phenols, flavonoids, and terpenoids). The 16S rRNA gene sequencing results indicated that the strain AD13-4 significantly affected the abundance and composition of the rhizospheric microbiota and improved soil activities and physiochemical properties. Our study provides theoretical support for the optimization of saline-alkali-tolerant PGPR and valuable information for elucidating the mechanism of plant alkaline-sodic tolerance.

Research on Physiological Characteristics and Differential Gene Expression of Rice Hybrids and Their Parents under Salt Stress at Seedling Stage

Soil salinization is one of the most important abiotic stresses which can seriously affect the growth and development of rice, leading to the decrease in or even loss of a rice harvest. Increasing the rice yield of saline soil is a key issue for agricultural production. The utilization of heterosis could significantly increase crop biomass and yield, which might be an effective way to meet the demand for rice cultivation in saline soil. In this study, to elucidate the regulatory mechanisms of rice hybrids and their parents that respond to salt stress, we investigated the phenotypic characteristics, physiological and biochemical indexes, and expression level of salt-related genes at the seedling stage. In this study, two sets of materials, encapsulating the most significant differences between the rice hybrids and their parents, were screened using the salt damage index and a hybrid superiority analysis. Compared with their parents, the rice hybrids Guang-Ba-You-Hua-Zhan (BB1) and Y-Liang-You-900 (GD1) exhibited much better salt tolerance, including an increased fresh weight and higher survival rate, a better scavenging ability towards reactive oxygen species (ROS), better ionic homeostasis with lower content of Na+ in their Na+/K+ ratio, and a higher expression of salt-stress-responsive genes. These results indicated that rice hybrids developed complex regulatory mechanisms involving multiple pathways and genes to adapt to salt stress and provided a physiological basis for the utilization of heterosis for improving the yield of rice under salt stress.

Smart reprograming of plants against salinity stress using modern biotechnological tools

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.

A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress

The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.

Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor

Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K⁺ and lower Na⁺ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K⁺/Na⁺ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.

Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin

Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

Physiological Measurements and Transcriptome Survey Reveal How Semi-mangrove Clerodendrum inerme Tolerates Saline Adversity

Salinity adversity has been a major environmental stressor for plant growth and reproduction worldwide. Semi-mangrove Clerodendrum inerme, a naturally salt-tolerant plant, can be studied as a successful example to understand the biological mechanism of saline resistance. Since it is a sophisticated and all-round scale process for plants to react to stress, our greenhouse study interpreted the response of C. inerme to salt challenge in the following aspects: morphology, osmotic protectants, ROS production and scavenging, ion homeostasis, photosynthetic efficiency, and transcriptome reprogramming. The results drew an overview picture to illustrate the tolerant performance of C. inerme from salt acclimatization (till medium NaCl level, 0.3 mol/L) to salinity stress (high NaCl level, 0.5 mol/L). The overall evaluation leads to a conclusion that the main survival strategy of C. inerme is globally reshaping metabolic and ion profiles to adapt to saline adversity. These findings uncover the defense mechanism by which C. inerme moderates its development rate to resist the short- and long-term salt adversity, along with rebalancing the energy allocation between growth and stress tolerance.

An Insight into Abiotic Stress and Influx Tolerance Mechanisms in Plants to Cope in Saline Environments

Simple Summary

This review focuses on plant growth and development harmed by abiotic stress, primarily salt stress. Salt stress raises the intracellular osmotic pressure, leading to hazardous sodium buildup. Plants react to salt stress signals by regulating ion homeostasis, activating the osmotic stress pathway, modulating plant hormone signaling, and altering cytoskeleton dynamics and cell wall composition. Understanding the processes underlying these physiological and biochemical responses to salt stress could lead to more effective agricultural crop yield measures. In this review, researchers outline recent advances in plant salt stress control. The study of plant salt tolerance processes is essential, both theoretically and practically, to improve agricultural output, produce novel salt-tolerant cultivars, and make full use of saline soil. Based on past research, this paper discusses the adverse effects of salt stress on plants, including photosynthesis suppression, ion homeostasis disturbance, and membrane peroxidation. The authors have also covered the physiological mechanisms of salt tolerance, such as the scavenging of reactive oxygen species and osmotic adjustment. This study further identifies specific salt stress-responsive mechanisms linked to physiological systems. Based on previous studies, this article reviews the current methodologies and techniques for improving plant salt tolerance. Overall, it is hoped that the above-mentioned points will impart helpful background information for future agricultural and crop plant production.

Abstract

Salinity is significant abiotic stress that affects the majority of agricultural, irrigated, and cultivated land. It is an issue of global importance, causing many socio-economic problems. Salt stress mainly occurs due to two factors: (1) soil type and (2) irrigation water. It is a major environmental constraint, limiting crop growth, plant productivity, and agricultural yield. Soil salinity is a major problem that considerably distorts ecological habitats in arid and semi-arid regions. Excess salts in the soil affect plant nutrient uptake and osmotic balance, leading to osmotic and ionic stress. Plant adaptation or tolerance to salinity stress involves complex physiological traits, metabolic pathways, the production of enzymes, compatible solutes, metabolites, and molecular or genetic networks. Different plant species have different salt overly sensitive pathways and high-affinity K⁺ channel transporters that maintain ion homeostasis. However, little progress has been made in developing salt-tolerant crop varieties using different breeding approaches. This review highlights the interlinking of plant morpho-physiological, molecular, biochemical, and genetic approaches to produce salt-tolerant plant species. Most of the research emphasizes the significance of plant growth-promoting rhizobacteria in protecting plants from biotic and abiotic stressors. Plant growth, survival, and yield can be stabilized by utilizing this knowledge using different breeding and agronomical techniques. This information marks existing research areas and future gaps that require more attention to reveal new salt tolerance determinants in plants—in the future, creating genetically modified plants could help increase crop growth and the toleration of saline environments.

Plant salt response: Perception, signaling, and tolerance

Salt stress is one of the significant environmental stressors that severely affects plant growth and development. Plant responses to salt stress involve a series of biological mechanisms, including osmoregulation, redox and ionic homeostasis regulation, as well as hormone or light signaling-mediated growth adjustment, which are regulated by different functional components. Unraveling these adaptive mechanisms and identifying the critical genes involved in salt response and adaption are crucial for developing salt-tolerant cultivars. This review summarizes the current research progress in the regulatory networks for plant salt tolerance, highlighting the mechanisms of salt stress perception, signaling, and tolerance response. Finally, we also discuss the possible contribution of microbiota and nanobiotechnology to plant salt tolerance.

Comparative transcriptomic and metabolic profiling provides insight into the mechanism by which the autophagy inhibitor 3-MA enhances salt stress sensitivity in wheat seedlings

BACKGROUND

Salt stress hinders plant growth and production around the world. Autophagy induced by salt stress helps plants improve their adaptability to salt stress. However, the underlying mechanism behind this adaptability remains unclear. To obtain deeper insight into this phenomenon, combined metabolomics and transcriptomics analyses were used to explore the coexpression of differentially expressed-metabolite (DEM) and gene (DEG) between control and salt-stressed wheat roots and leaves in the presence or absence of the added autophagy inhibitor 3-methyladenine (3-MA).

RESULTS

The results indicated that 3-MA addition inhibited autophagy, increased ROS accumulation, damaged photosynthesis apparatus and impaired the tolerance of wheat seedlings to NaCl stress. A total of 14,759 DEGs and 554 DEMs in roots and leaves of wheat seedlings were induced by salt stress. DEGs were predominantly enriched in cellular amino acid catabolic process, response to external biotic stimulus, regulation of the response to salt stress, reactive oxygen species (ROS) biosynthetic process, regulation of response to osmotic stress, ect. The DEMs were mostly associated with amino acid metabolism, carbohydrate metabolism, phenylalanine metabolism, carbapenem biosynthesis, and pantothenate and CoA biosynthesis. Further analysis identified some critical genes (gene involved in the oxidative stress response, gene encoding transcription factor (TF) and gene involved in the synthesis of metabolite such as alanine, asparagine, aspartate, glutamate, glutamine, 4-aminobutyric acid, abscisic acid, jasmonic acid, ect.) that potentially participated in a complex regulatory network in the wheat response to NaCl stress. The expression of the upregulated DEGs and DEMs were higher, and the expression of the down-regulated DEGs and DEMs was lower in 3-MA-treated plants under NaCl treatment.

CONCLUSION

3-MA enhanced the salt stress sensitivity of wheat seedlings by inhibiting the activity of the roots and leaves, inhibiting autophagy in the roots and leaves, increasing the content of both H₂O₂ and O₂•-, damaged photosynthesis apparatus and changing the transcriptome and metabolome of salt-stressed wheat seedlings.

Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

Food Security and Sustainability: Discussing the Four Pillars to Encompass Other Dimensions

The unadjusted intake of food constitutes a real challenge for the several sustainability dimensions. In this perspective, the main objectives of this research are to characterise the current contexts of food security, its relationship with sustainability, and identify proposals and actions that may support the design of more adjusted policies in the future. In addition, it is intended to assess if the food security pillars properly address the sustainability goals and if the evolution of undernutrition is accompanied by sustainable frameworks. In this way, statistical information from the FAOSTAT database was considered for the several dimensions of food security over the period 2000-2020. These data were analysed through factor-cluster approaches and panel data methodologies, namely those related to quantile regressions. As main insights, we may refer that undernutrition is more impacted by the availability of food and nutrients and political stability than by the level of GDP-Gross Domestic Product (except for the extreme cases). This means that the level of development is not the primary explanation for the problems of nutrition. The main focus of the national and international policies must be to improve the agrifood supply chains and to support political stability, in order to mitigate undernutrition worldwide and ensure a global access to sustainable and healthy diets. In addition, it is suggested to rethink the four pillars of food security (availability, access, utilisation and stability), in order to encompass other dimensions, such as climate change.

Regulation of Plant Responses to Salt Stress

Salt stress is a major environmental stress that affects plant growth and development. Plants are sessile and thus have to develop suitable mechanisms to adapt to high-salt environments. Salt stress increases the intracellular osmotic pressure and can cause the accumulation of sodium to toxic levels. Thus, in response to salt stress signals, plants adapt via various mechanisms, including regulating ion homeostasis, activating the osmotic stress pathway, mediating plant hormone signaling, and regulating cytoskeleton dynamics and the cell wall composition. Unraveling the mechanisms underlying these physiological and biochemical responses to salt stress could provide valuable strategies to improve agricultural crop yields. In this review, we summarize recent developments in our understanding of the regulation of plant salt stress.

Monitoring of Salinity, Temperature, and Drought Stress in Grafted Watermelon Seedlings Using Chlorophyll Fluorescence

Chlorophyll fluorescence (CF) is used to measure the physiological status of plants affected by biotic and abiotic stresses. Therefore, we aimed to identify the changes in CF parameters in grafted watermelon seedlings exposed to salt, drought, and high and low temperatures. Grafted watermelon seedlings at the true three-leaf stage were subjected to salinity levels (0, 50, 100, 150, and 200 mM) and temperature [low (8°C), moderate (24°C), and high (40°C)] stresses for 12 days under controlled environmental conditions independently. Eight CF parameters were measured at 2-day intervals using the FluorCam machine quenching protocol of the FluorCam machine. The seedlings were also exposed to drought stress for 3 days independent of salinity and temperature stress; CF parameters were measured at 1-day intervals. In addition, growth parameters, proline, and chlorophyll content were evaluated in all three experiments. The CF parameters were differentially influenced depending on the type and extent of the stress conditions. The results showed a notable effect of salinity levels on CF parameters, predominantly in maximum quantum yield (Fv/Fm), non-photochemical quenching (NPQ), the ratio of the fluorescence decrease (Rfd), and quantum yield of non-regulated energy dissipation in PSII [Y(NO)]. High temperature had significant effects on Rfd and NPQ, whereas low temperature showed significant results in most CF parameters: Fv/Fm, Y(NO), NPQ, Rfd, the efficiency of excitation capture of open photosystem II (PSII) center (Fv'/Fm'), and effective quantum yield of photochemical energy conversion in PSII [Y(PSII)]. Only NPQ and Rfd were significantly influenced by severe drought stress. Approximately, all the growth parameters were significantly influenced by the stress level. Proline content increased with an increase in stress levels in all three experiments, whereas the chlorophyll (a and b) content either decreased or increased depending upon the stressor. The results provided here may be useful for understanding the effect of abiotic stresses on CF parameters and the selection of index CF parameters to detect abiotic stresses in grafted watermelon seedlings.