Auxin-mediated responses under salt stress: from developmental regulation to biotechnological applications

Surviving the Stress: Understanding the Molecular Basis of Plant Adaptations and Uncovering the Role of Mycorrhizal Association in Plant Abiotic Stresses

Environmental stresses severely impair plant growth, resulting in significant crop yield and quality loss. Among various abiotic factors, salt and drought stresses are one of the major factors that affect the nutrients and water uptake by the plants, hence ultimately various physiological aspects of the plants that compromises crop yield. Continuous efforts have been made to investigate, dissect and improve plant adaptations at the molecular level in response to drought and salinity stresses. In this context, the plant beneficial microbiome presents in the rhizosphere, endosphere, and phyllosphere, also referred as second genomes of the plant is well known for its roles in plant adaptations. Exploration of beneficial interaction of fungi with host plants known as mycorrhizal association is one such special interaction that can facilitates the host plants adaptations. Mycorrhiza assist in alleviating the salinity and drought stresses of plants via redistributing the ion imbalance through translocation to different parts of the plants, as well as triggering oxidative machinery. Mycorrhiza association also regulates the level of various plant growth regulators, osmolytes and assists in acquiring minerals that are helpful in plant's adaptation against extreme environmental stresses. The current review examines the role of various plant growth regulators and plants' antioxidative systems, followed by mycorrhizal association during drought and salt stresses.

Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

Comparative Transcriptome Analysis Revealed Candidate Gene Modules Involved in Salt Stress Response in Sweet Basil and Overexpression of ObWRKY16 and ObPAL2 Enhanced Salt Tolerance of Transgenic Arabidopsis

Sweet basil (Ocimum basilicum L.) is an important aromatic plant with high edibility and economic value, widely distributed in many regions of the tropics including the south of China. In recent years, environmental problems, especially soil salinization, have seriously restricted the planting and spread of sweet basil. However, the molecular mechanism of the salt stress response in sweet basil is still largely unknown. In this study, seed germination, seedling growth, and chlorophyll synthesis in sweet basil were inhibited under salt stress conditions. Through comparative transcriptome analysis, the gene modules involved in the metabolic processes, oxidative response, phytohormone signaling, cytoskeleton, and photosynthesis were screened out. In addition, the landscape of transcription factors during salt treatment in sweet basil was displayed as well. Moreover, the overexpression of the WRKY transcription factor-encoding gene, ObWRKY16, and the phenylalanine ammonia-lyase-encoding gene, ObPAL2, enhanced the seed germination, seedling growth, and survival rate, respectively, of transgenic Arabidopsis, suggesting that they might be important candidates for the creation of salt-tolerant sweet basil cultivars. Our data enrich the study on salt responses in sweet basil and provide essential gene resources for genetic improvements in sweet basil in the future.

Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice

Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.

Metabolome and Transcriptome Analysis Revealed the Pivotal Role of Exogenous Melatonin in Enhancing Salt Tolerance in Vitis vinifera L

Vitis vinifera L. possesses high economic value, but its growth and yield are seriously affected by salt stress. Though melatonin (MT) has been widely reported to enhance tolerance towards abiotic stresses in plants, the regulatory role melatonin plays in resisting salt tolerance in grapevines has scarcely been studied. Here, we observed the phenotypes under the treatment of different melatonin concentrations, and then transcriptome and metabolome analyses were performed. A total of 457 metabolites were detected in CK- and MT-treated cell cultures at 1 WAT (week after treatment) and 4 WATs. Exogenous melatonin treatment significantly increased the endogenous melatonin content while down-regulating the flavonoid content. To be specific, the melatonin content was obviously up-regulated, while the contents of more than a dozen flavonoids were down-regulated. Auxin response genes and melatonin synthesis-related genes were regulated by the exogenous melatonin treatment. WGCNA (weighted gene coexpression network analysis) identified key salt-responsive genes; they were directly or indirectly involved in melatonin synthesis and auxin response. The synergistic effect of salt and melatonin treatment was investigated by transcriptome analysis, providing additional evidence for the stress-alleviating properties of melatonin through auxin-related pathways. The present study explored the impact of exogenous melatonin on grapevines' ability to adapt to salt stress and provided novel insights into enhancing their tolerance to salt stress.

Potential Response Patterns of Endogenous Hormones in Cliff Species Opisthopappus taihangensis and Opisthopappus longilobus under Salt Stress

When plants are exposed to salt stress, endogenous hormones are essential for their responses through biosynthesis and signal transduction pathways. However, the roles of endogenous hormones in two cliff species (Opisthopappus taihangensis and Opisthopappus longilobus (Opisthopappus genus)) in the Taihang Mountains under salt stress have not been investigated to date. Following different time treatments under 500 mM salt concentrations, 239 differentially expressed gene (DEG)-related endogenous hormones were identified that exhibited four change trends, which in Profile 47 were upregulated in both species. The C-DEG genes of AUX, GA, JA, BR, ETH, and ABA endogenous hormones were significantly enriched in Opisthopappus taihangensis (O. taihangensis) and Opisthopappus longilobus (O. longilobus). During the responsive process, mainly AUX, GA, and JA biosynthesis and signal transduction were triggered in the two species. Subsequently, crosstalk further influenced BR, EHT, ABA, and MAPK signal transduction pathways to improve the salt resistance of the two species. Within the protein-protein interactions (PPI), seven proteins exhibited the highest interactions, which primarily involved two downregulated genes (SAUR and GA3ox) and eight upregulated genes (ACX, MFP2, JAZ, BRI1, BAK1, ETR, EIN2, and SNRK2) of the above pathways. The more upregulated expression of ZEP (in the ABA biosynthesis pathway), DELLA (in the GA signaling pathway), ABF (in the ABA signaling pathway), and ERF1 (in the ETH signaling pathway) in O. taihangensis revealed that it had a relatively higher salt resistance than O. longilobus. This revealed that the responsive patterns to salt stress between the two species had both similarities and differences. The results of this investigation shed light on the potential adaptive mechanisms of O. taihangensis and O. longilobus under cliff environments, while laying a foundation for the study of other cliff species in the Taihang Mountains.

Codium fragile (Suringar) Hariot as Biostimulant Agent to Alleviate Salt Stress in Durum Wheat: Preliminary Results from Germination Trials

Soil salinization is a critical environmental problem in arid and semiarid regions of the world. The aim of the present study was to evaluate the effect of an algae-based biostimulant on germination and seedling vigour of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.), under different saline conditions (0, 100, and 200 mM NaCl). The experiment was carried out under controlled-environment conditions. Seeds were sprayed with a solution containing a combination of fungicide and different concentrations of Codium fragile (Suringar) Hariot algae (0%w/v, 10%w/v, 20%w/v, and 30%w/v). All experimental units were placed in a germination cabinet. The effect of the seaweed extract (SWE) on seed germination and seedling performance under salinity stress was evaluated over a period of 8 days. Coleoptile length and biomass were found to be significantly and positively affected by the application of different SWE doses as compared to the control treatment (0% algae). As for germination traits, seeds treated with SWE showed a final germination (from 82% to 88%), under severe saline conditions, significantly higher than that observed in the control treatment (61%). Our findings indicate that the appropriate dose of biostimulant can markedly improve the germination and the seedlings vigour of durum wheat seeds under saline conditions. Additional studies will be needed to understand the mechanism of action of this biostimulant and its effectiveness in longer studies under field conditions.

Endogenous melatonin involved in plant salt response by impacting auxin signaling

KEY MESSAGE

The study on melatonin biosynthesis mutant snat1snat2 revealed that endogenous melatonin plays an important role in salt responsiveness by mediating auxin signaling. Melatonin is a pleiotropic signaling molecule, which, besides being involved in multiple growth and developmental processes, also mediates environmental stress responses. However, whether and how endogenous melatonin is involved in salt response has not been determined. In this study, we elucidated the involvement of endogenous melatonin in salt response by investigatiing the impact of salt stress on a double mutant of Arabidopsis (snat1snat2) defective in melatonin biosynthesis genes SNAT1 and SNAT2. This mutant was found to exhibit salt sensitivity, manifested by unhealthy growth, ion imbalance and ROS accumulation under salt stress. Transcriptomic profiles of snat1snat2 revealed that the expression of a large number of salt-responsive genes was affected by SNAT defect, and these genes were closely related to the synthesis of auxin and several signaling pathways. In addition, the salt-sensitive growth phenotype of snat1snat2 was alleviated by the application of exogenous auxin. Our results show that endogenous melatonin may be essential for plant salt tolerance, a function that could be correlated with diverse activity in mediating auxin signaling.

Modulation of antioxidant defense and PSII components by exogenously applied acetate mitigates salinity stress in Avena sativa

Salinity stress has detrimental effects on various aspects of plant development. However, our understanding of strategies to mitigate these effects in crop plants remains limited. Recent research has shed light on the potential of sodium acetate as a mitigating component against salinity stress in several plant species. Here, we show the role of acetate sodium in counteracting the adverse effects on oat (Avena sativa) plants subjected to NaCl-induced salinity stress, including its impact on plant morphology, photosynthetic parameters, and gene expression related to photosynthesis and antioxidant capacity, ultimately leading to osmoprotection. The five-week experiment involved subjecting oat plants to four different conditions: water, salt (NaCl), sodium acetate, and a combination of salt and sodium acetate. The presence of NaCl significantly inhibited plant growth and root elongation, disrupted chlorophylls and carotenoids content, impaired chlorophyll fluorescence, and down-regulated genes associated with the plant antioxidant defense system. Furthermore, our findings reveal that when stressed plants were treated with sodium acetate, it partially reversed these adverse effects across all analyzed parameters. This reversal was particularly evident in the increased content of proline, thereby ensuring osmoprotection for oat plants, even under stressful conditions. These results provide compelling evidence regarding the positive impact of sodium acetate on various plant development parameters, with a particular focus on the enhancement of photosynthetic activity.

Auxin and abiotic stress responses

Plants are exposed to a variety of abiotic stresses; these stresses have profound effects on plant growth, survival, and productivity. Tolerance and adaptation to stress require sophisticated stress sensing, signaling, and various regulatory mechanisms. The plant hormone auxin is a key regulator of plant growth and development, playing pivotal roles in the integration of abiotic stress signals and control of downstream stress responses. In this review, we summarize and discuss recent advances in understanding the intersection of auxin and abiotic stress in plants, with a focus on temperature, salt, and drought stresses. We also explore the roles of auxin in stress tolerance and opportunities arising for agricultural applications.

Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L

Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance.

SlSAMS1 enhances salt tolerance through regulation DNA methylation of SlGI in tomato

S-adenosylmethionine (SAM), which is synthesized from methionine and ATP catalyzed by S-adenosylmethionine synthetase (SAMS), is an important methyl donor in plants. SAMS and DNA methylation play an important role in the plant response to abiotic stresses. Previous studies have shown that SAMS improves salt tolerance in tomato plants, but it is not clear whether the DNA methylation pathway mediates SAMS-induced salt tolerance. This study confirmed that SlSAMS1-overexpressing plants exhibited improved salt tolerance. Through whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing (RNA-seq) analysis, the study screened the circadian rhythm pathway and identified the gene SlGI in this pathway, which was regulated by SlSAMS1. The gene body region of SlGI, the core gene of the circadian rhythm pathway, was hypermethylated in SlSAMS1-overexpressing plants, and its expression level was significantly increased. Furthermore, the SlGI-overexpressing plants showed higher salt tolerance, less reduction in plant height and fresh weight, lower electrolyte leakage, malondialdehyde and H2O2 content, and higher antioxidant enzyme activity compared to wild type plants. Therefore, SlSAMS1-overexpressing plants regulated significant changes in CHG-type methylation sites of the SlGI gene body and its expression levels, leading to an enhanced salt tolerance of tomato plants.

Halomonas ventosae JPT10 promotes salt tolerance in foxtail millet (Setaria italica) by affecting the levels of multiple antioxidants and phytohormones

Plant growth-promoting bacterias (PGPBs) can increase crop output under normal and abiotic conditions. However, the mechanisms underlying the plant salt tolerance-promoting role of PGPBs still remain largely unknown. In this study, we demonstrated that Halomonas ventosae JPT10 promoted the salt tolerance of both dicots and monocots. Physiological analysis revealed that JPT10 reduced reactive oxygen species accumulation by improving the antioxidant capability of foxtail millet seedlings. The metabolomic analysis of JPT10-inoculated foxtail millet seedlings led to the identification of 438 diversely accumulated metabolites, including flavonoids, phenolic acids, lignans, coumarins, sugar, alkaloids, organic acids, and lipids, under salt stress. Exogenous apigenin and chlorogenic acid increased the salt tolerance of foxtail millet seedlings. Simultaneously, JPT10 led to greater amounts of abscisic acid (ABA), indole-3-acetic acid (IAA), salicylic acid (SA), and their derivatives but lower levels of 12-oxo-phytodienoic acid (OPDA), jasmonate (JA), and JA-isoleucine (JA-Ile) under salt stress. Exogenous JA, methyl-JA, and OPDA intensified, whereas ibuprofen or phenitone, two inhibitors of JA and OPDA biosynthesis, partially reversed, the growth inhibition of foxtail millet seedlings caused by salt stress. Our results shed light on the response of foxtail millet seedlings to H. ventosae under salt stress and provide potential compounds to increase salt tolerance in foxtail millet and other crops.

A complex signaling trio in seed germination: Auxin-JA-ABA

Recently. Mei et al. discovered the molecular mechanism behind the synergistic action of auxins and jasmonates in enhancing the role of abscisic acid (ABA) in seed germination. They found that JASMONATE-ZIM DOMAIN (JAZ) proteins interact with AUXIN RESPONSE FACTOR (ARF)-16 to mediate auxin-jasmonic acid (JA) crosstalk. Furthermore, they revealed that ARF16 interacts with ABSCISIC ACID INSENSITIVE (ABI)-5 and positively modulates ABA responses at seed germination.

How Plants Tolerate Salt Stress

Soil salinization inhibits plant growth and seriously restricts food security and agricultural development. Excessive salt can cause ionic stress, osmotic stress, and ultimately oxidative stress in plants. Plants exclude excess salt from their cells to help maintain ionic homeostasis and stimulate phytohormone signaling pathways, thereby balancing growth and stress tolerance to enhance their survival. Continuous innovations in scientific research techniques have allowed great strides in understanding how plants actively resist salt stress. Here, we briefly summarize recent achievements in elucidating ionic homeostasis, osmotic stress regulation, oxidative stress regulation, and plant hormonal responses under salt stress. Such achievements lay the foundation for a comprehensive understanding of plant salt-tolerance mechanisms.

Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva

MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs-mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca²⁺ signaling, and oxidative defense signaling pathways are involved in H. fulva's response to NaCl stress.

Transcriptome Reveals the Molecular Mechanism of the ScALDH21 Gene from the Desert Moss Syntrichia caninervis Conferring Resistance to Salt Stress in Cotton

The desert moss Syntrichia caninervis has proven to be an excellent plant material for mining resistance genes. The aldehyde dehydrogenase 21 (ScALDH21) gene from S. caninervis has been shown to confer tolerance to salt and drought, but it is unclear how the transgene ScALDH21 regulates tolerance to abiotic stresses in cotton. In the present work, we studied the physiological and transcriptome analyses of non-transgenic (NT) and transgenic ScALDH21 cotton (L96) at 0 day, 2 days, and 5 days after salt stress. Through intergroup comparisons and a weighted correlation network analysis (WGCNA), we found that there were significant differences between NT and L96 cotton in the plant hormone, Ca2+, and mitogen-activated protein kinase (MAPK) signaling pathways as well as for photosynthesis and carbohydrate metabolism. Overexpression of ScALDH21 significantly increased the expression of stress-related genes in L96 compared to NT cotton under both normal growth and salt stress conditions. These data suggest that the ScALDH21 transgene can scavenge more reactive oxygen species (ROS) in vivo relative to NT cotton and improve cotton resistance to salt stress by increasing the expression of stress-responsive genes, responding quickly to stress stimuli, enhancing photosynthesis and improving carbohydrate metabolism. Therefore, ScALDH21 is a promising candidate gene to improve resistance to salt stress, and the application of this gene in cotton provides new insights into molecular plant breeding.

Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene in Gossypium

Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germination, and responses to biotic and abiotic environments. In this study, 146 Gossypium hirsutum, 138 Gossypium barbadense, 89 Gossypium arboreum and 84 Gossypium raimondii SBTs were identified and divided into six subfamilies. Cotton SBTs are unevenly distributed on chromosomes. Synteny analysis showed that the members of SBT1 and SBT4 were expanded in cotton compared to Arabidopsis thaliana. Co-expression network analysis showed that six Gossypium arboreum SBT gene family members were in a network, among which five SBT1 genes and their Gossypium hirsutum and Arabidopsis thaliana direct homologues were down-regulated by salt treatment, indicating that the co-expression network might share conserved functions. Through co-expression network and annotation analysis, these SBTs may be involved in the biological processes of auxin transport, ABA signal transduction, cell wall repair and root tissue development. In summary, this study provides valuable information for the study of SBT genes in cotton and excavates SBT genes in response to salt stress, which provides ideas for cotton breeding for salinity resistance.

Auxin contributes to jasmonate-mediated regulation of abscisic acid signaling during seed germination in Arabidopsis

Abscisic acid (ABA) represses seed germination and postgerminative growth in Arabidopsis thaliana. Auxin and jasmonic acid (JA) stimulate ABA function; however, the possible synergistic effects of auxin and JA on ABA signaling and the underlying molecular mechanisms remain elusive. Here, we show that exogenous auxin works synergistically with JA to enhance the ABA-induced delay of seed germination. Auxin biosynthesis, perception, and signaling are crucial for JA-promoted ABA responses. The auxin-dependent transcription factors AUXIN RESPONSE FACTOR10 (ARF10) and ARF16 interact with JASMONATE ZIM-DOMAIN (JAZ) repressors of JA signaling. ARF10 and ARF16 positively mediate JA-increased ABA responses, and overaccumulation of ARF16 partially restores the hyposensitive phenotype of JAZ-accumulating plants defective in JA signaling in response to combined ABA and JA treatment. Furthermore, ARF10 and ARF16 physically associate with ABSCISIC ACID INSENSITIVE5 (ABI5), a critical regulator of ABA signaling, and the ability of ARF16 to stimulate JA-mediated ABA responses is mainly dependent on ABI5. ARF10 and ARF16 activate the transcriptional function of ABI5, whereas JAZ repressors antagonize their effects. Collectively, our results demonstrate that auxin contributes to the synergetic modulation of JA on ABA signaling, and explain the mechanism by which ARF10/16 coordinate with JAZ and ABI5 to integrate the auxin, JA, and ABA signaling pathways.

Genome-Wide Identification of 2-Oxoglutarate and Fe (II)-Dependent Dioxygenase (2ODD-C) Family Genes and Expression Profiles under Different Abiotic Stresses in Camellia sinensis (L.)

The 2-oxoglutarate and Fe (II)-dependent dioxygenase (2ODD-C) family of 2-oxoglutarate-dependent dioxygenases potentially participates in the biosynthesis of various metabolites under various abiotic stresses. However, there is scarce information on the expression profiles and roles of 2ODD-C genes in Camellia sinensis. We identified 153 Cs2ODD-C genes from C. sinensis, and they were distributed unevenly on 15 chromosomes. According to the phylogenetic tree topology, these genes were divided into 21 groups distinguished by conserved motifs and an intron/exon structure. Gene-duplication analyses revealed that 75 Cs2ODD-C genes were expanded and retained after WGD/segmental and tandem duplications. The expression profiles of Cs2ODD-C genes were explored under methyl jasmonate (MeJA), polyethylene glycol (PEG), and salt (NaCl) stress treatments. The expression analysis showed that 14, 13, and 49 Cs2ODD-C genes displayed the same expression pattern under MeJA and PEG treatments, MeJA and NaCl treatments, and PEG and NaCl treatments, respectively. A further analysis showed that two genes, Cs2ODD-C36 and Cs2ODD-C21, were significantly upregulated and downregulated after MeJA, PEG, and NaCl treatments, indicating that these two genes played positive and negative roles in enhancing the multi-stress tolerance. These results provide candidate genes for the use of genetic engineering technology to modify plants by enhancing multi-stress tolerance to promote phytoremediation efficiency.

Nitrogen application improves salt tolerance of grape seedlings via regulating hormone metabolism

Salt stress is a dominant environmental factor that restricts the growth and yield of crops. Nitrogen is an essential mineral element for plants, regulates various physiological and biochemical processes, and has been reported to enhance salt tolerance in plants. However, the crosstalk between salt and nitrogen in grapes is not well understood. In this study, we found that nitrogen supplementation (0.01 and 0.1 mol L-1 NH4 NO3 ) significantly increased the accumulation of proline, chlorophyll, Na+ , NH4 + , and NO3 - , while it reduced the malondialdehyde content and inhibited photosynthetic performance under salt stress conditions (200 mmol L-1 NaCl). Further transcriptome and metabolome analyses showed that a total of 4890 differentially expressed genes (DEGs) and 753 differently accumulated metabolites (DAMs) were identified. Joint omics results revealed that plant hormone signal transduction pathway connected the DEGs and DAMs. In-depth analysis revealed that nitrogen supplementation increased the levels of endogenous abscisic acid, salicylic acid, and jasmonic acid by inducing the expression of 11, 4, and 13 genes related to their respective biosynthesis pathway. In contrast, endogenous indoleacetic acid content was significantly reduced due to the remarkable regulation of seven genes of its biosynthetic pathway. The modulation in hormone contents subsequently activated the differential expression of 13, 10, 12, and 29 genes of the respective downstream hormone signaling transduction pathways. Overall, all results indicate that moderate nitrogen supplementation could improve salt tolerance by regulating grape physiology and endogenous hormone homeostasis, as well as the expression of key genes in signaling pathways, which provides new insights into the interactions between mineral elements and salt stress.

Starch and Sucrose Metabolism and Plant Hormone Signaling Pathways Play Crucial Roles in Aquilegia Salt Stress Adaption

Salt stress is one of the main abiotic stresses that strongly affects plant growth. Clarifying the molecular regulatory mechanism in ornamental plants under salt stress is of great significance for the ecological development of saline soil areas. Aquilegia vulgaris is a perennial with a high ornamental and commercial value. To narrow down the key responsive pathways and regulatory genes, we analyzed the transcriptome of A. vulgaris under a 200 mM NaCl treatment. A total of 5600 differentially expressed genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis pointed out that starch and sucrose metabolism and plant hormone signal transduction were significantly improved. The above pathways played crucial roles when A. vulgaris was coping with salt stress, and their protein-protein interactions (PPIs) were predicted. This research provides new insights into the molecular regulatory mechanism, which could be the theoretical basis for screening candidate genes in Aquilegia.

IAA Plays an Important Role in Alkaline Stress Tolerance by Modulating Root Development and ROS Detoxifying Systems in Rice Plants

Auxin regulates plant growth and development, as well as helps plants to survive abiotic stresses, but the effects of auxin on the growth of alkaline-stressed rice and the underlying molecular and physiological mechanisms remain unknown. Through exogenous application of IAA/TIBA, this study explored the physiological and molecular mechanisms of alkaline stress tolerance enhancement using two rice genotypes. Alkaline stress was observed to damage the plant growth, while exogenous application of IAA mitigates the alkaline-stress-induce inhibition of plant growth. After application of exogenous IAA to alkaline-stressed rice, dry shoot biomass, foliar chlorophyll content, photosynthetic rate in the two rice genotypes increased by 12.6-15.6%, 11.7-40.3%, 51.4-106.6%, respectively. The adventitious root number, root surface area, total root length and dry root biomass in the two rice genotypes increased by 29.3-33.3%, 26.4-27.2%, 42.5-35.5% and 12.8-33.1%, respectively. The accumulation of H₂O₂, MAD were significantly decreased with the application of IAA. The activities of CAT, POD, and SOD in rice plants were significantly increased by exogenous application of IAA. The expression levels of genes controlling IAA biosynthesis and transport were significantly increased, while there were no significant effects on the gene expression that controlled IAA catabolism. These results showed that exogenous application of IAA could mitigate the alkaline-stress-induced inhibition of plant growth by regulating the reactive oxygen species scavenging system, root development and expression of gene involved in IAA biosynthesis, transport and catabolism. These results provide a new direction and empirical basis for improving crop alkaline tolerance with exogenous application of IAA.

PIN1 regulates epidermal cells development under drought and salt stress using single-cell analysis

Over the course of evolution, plants have developed plasticity to acclimate to environmental stresses such as drought and salt stress. These plant adaptation measures involve the activation of cascades of molecular networks involved in stress perception, signal transduction and the expression of stress related genes. Here, we investigated the role of the plasma membrane-localized transporter of auxin PINFORMED1 (PIN1) in the regulation of pavement cells (PCs) and guard cells (GCs) development under drought and salt stress conditions. The results showed that drought and salt stress treatment affected the development of PCs and GCs. Further analysis identified the different regulation mechanisms of PIN1 in regulating the developmental patterns of PCs and GCs under drought and salt stress conditions. Drought and salt stress also regulated the expression dynamics of PIN1 in pif1/3/4/5 quadruple mutants. Collectively, we revealed that PIN1 plays a crucial role in regulating plant epidermal cells development under drought and salt stress conditions, thus contributing to developmental rebustness and plasticity.

Transcriptome analysis of perennial ryegrass reveals the regulatory role of Aspergillus aculeatus under salt stress

Perennial ryegrass (Lolium perenne) is an important turf grass and forage grass with moderately tolerant to salinity stress. Aspergillus aculeatus has been documented to involved in salt stress response of perennial ryegrass, while the A. aculeatus-mediated molecular mechanisms are unclear. Therefore, to investigate the molecular mechanisms underlying A. aculeatus-mediated salt tolerance, the comprehensive transcriptome analysis of the perennial ryegrass roots was performed. Twelve cDNA libraries from roots were constructed after 12 h of plant-fungus cocultivation under 300 mM salt stress concentrations. A total of 21,915 differentially expressed genes (DEGs) were identified through pairwise comparisons. Enrichment analysis revealed that potentially important A. aculeatus-induced salt responsive genes belonging to specific categories, such as hormonal metabolism (auxin and salicylic acid metabolism related genes), secondary metabolism (flavonoid's metabolism related genes) and transcription factors (MYB, HSF and AP2/EREBP family). In addition, weighted gene co-expression network analysis (WGCNA) showed that blue and black modules were significantly positively correlated with the peroxidase activity and proline content, then the hub genes within these two modules were further identified. Taken together, we found the categories of A. aculeatus-induced salt responsive genes, revealing underlying fungus-induced molecular mechanisms of salt stress response in perennial ryegrass roots. Besides, fungus-induced salt-tolerant hub genes represent a foundation for further exploring the molecular mechanisms.

Coastal Wild Grapevine Accession (Vitis vinifera L. ssp. sylvestris) Shows Distinct Late and Early Transcriptome Changes under Salt Stress in Comparison to Commercial Rootstock Richter 110

Increase in soil salinity, driven by climate change, is a widespread constrain for viticulture across several regions, including the Mediterranean basin. The implementation of salt-tolerant varieties is sought after to reduce the negative impact of salinity in grape production. An accession of wild grapevine (Vitis vinifera L. ssp. sylvestris), named AS1B, found on the coastline of Asturias (Spain), could be of interest toward the achievement of salt-tolerant varieties, as it demonstrated the ability to survive and grow under high levels of salinity. In the present study, AS1B is compared against widely cultivated commercial rootstock Richter 110, regarding their survival capabilities, and transcriptomic profiles analysis allowed us to identify the genes by employing RNA-seq and gene ontology analyses under increasing salinity and validate (via RT-qPCR) seven salinity-stress-induced genes. The results suggest contrasting transcriptomic responses between AS1B and Richter 110. AS1B is more responsive to a milder increase in salinity and builds up specific mechanisms of tolerance over a sustained salt stress, while Richter 110 maintains a constitutive expression until high and prolonged saline inputs, when it mainly shows responses to osmotic stress. The genetic basis of AS1B's strategy to confront salinity could be valuable in cultivar breeding programs, to expand the current range of salt-tolerant rootstocks, aiming to improve the adaptation of viticulture against climate change.

Identification of the bZIP gene family and regulation of metabolites under salt stress in isatis indigotica

The bZIP transcription factor family plays important roles in plant growth and development, response to stress, and regulation of secondary metabolite biosynthesis. The identification and molecular function of bZIP gene have been deeply studied in the model plant Arabidopsis thaliana, but it has not been reported in the medicinal plant Isatis indigotica. In this study, 65 IibZIP genes were identified in the genome of I. indigotica, which were distributed on seven chromosomes, were highly conserved, could be classified into 11 subgroups. Transcriptomic and metabolomic data for leaves of I. indigotica exposed to salt stress were analyzed to construct an IibZIP gene co-expression network and metabolite correlation network. Seventeen IibZIP genes were co-expressed with 79 transcription factors, and GO and KEGG enrichment analysis showed that most of these genes were associated with abiotic stress and hormone responses of plants. 17 IibZIP genes regulated 110 metabolites through 92 transcription factor associations. In addition, IibZIP23, IibZIP38 and IibZIP51 were associated with six metabolites including three alkaloids (quinoline alkaloid stylopine, indole alkaloids tabersonine and indole-3-acetic acid), flavonoid myricetin 3-O-galactoside, and two primary metabolites 2-hydroxy-6-aminopurine, 3-dehydroshikimic acid were strongly correlated. This study provides data for identification of the IibZIP gene family and their regulation of metabolites in response to salt stress.

De novo transcriptome analysis of high-salinity stress-induced antioxidant activity and plant phytohormone alterations in Sesuvium portulacastrum

Sesuvium portulacastrum has a strong salt tolerance and can grow in saline and alkaline coastal and inland habitats. This study investigated the physiological and molecular responses of S. portulacastrum to high salinity by analyzing the changes in plant phytohormones and antioxidant activity, including their differentially expressed genes (DEGs) under similar high-salinity conditions. High salinity significantly affected proline (Pro) and hydrogen peroxide (H2O2) in S. portulacastrum seedlings, increasing Pro and H2O2 contents by 290.56 and 83.36%, respectively, compared to the control. Antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), significantly increased by 83.05, 205.14, and 751.87%, respectively, under high salinity. Meanwhile, abscisic acid (ABA) and gibberellic acid (GA3) contents showed the reverse trend of high salt treatment. De novo transcriptome analysis showed that 36,676 unigenes were matched, and 3,622 salt stress-induced DEGs were identified as being associated with the metabolic and biological regulation processes of antioxidant activity and plant phytohormones. POD and SOD were upregulated under high-salinity conditions. In addition, the transcription levels of genes involved in auxin (SAURs and GH3), ethylene (ERF1, ERF3, ERF114, and ABR1), ABA (PP2C), and GA3 (PIF3) transport or signaling were altered. This study identified key metabolic and biological processes and putative genes involved in the high salt tolerance of S. portulacastrum and it is of great significance for identifying new salt-tolerant genes to promote ecological restoration of the coastal strand.

Transcriptomic profiling revealed the role of 24-epibrassinolide in alleviating salt stress damage in tall fescue (Festuca arundinacea)

Soil salinization is a major problem all over the world. The accumulation of salt in soil reduces the root water uptake and directly affects plant growth and metabolic activities. Brassinosteroid is a plant hormone that plays an important role in regulation of plant growth and physiological process, including promotion of cell expansion and elongation, signal transduction and stress response. Exogenous 24-epibrassinolide (EBL) has been proved to alleviate various environmental stress in plants. However, the role that EBL plays in salt stress response is still unknown in tall fescue (Festuca arundinacea). In this study, the physiology and molecular mechanisms regulated by exogenous EBL of salt stress response in tall fescue was investigated. Tall fescue plants were divided into four groups, including control (CK), NaCl solution (SALT), 24-epibrassinolide (EBL), NaCl solution + 24-epibrassinolide (SE). During the growth period of tall fescue, we found that electrolyte leakage (EL) and malondialdehyde (MDA) were decreased, chlorophyll (Chl) content and antioxidant enzyme activity were increased in leaves of tall fescue in SE group compared with SALT group, indicating that EBL improved the salt tolerance in grasses. Transcriptomic profiling analysis showed that after 12 h of treatments, 10,265, 13,830 and 10,537 differential genes were expressed in EBL, SALT, and SE groups compared with control, respectively. These differentially expressed genes (DEGs) mainly focused on binding, catalytic activity, cellular process, metabolic process, cellular anatomical entity. Moreover, most of the differential genes were expressed in the plant hormone signal transduction pathway. These results helped us to better understand the mechanism of exogenous 24-epibrassinolide to improve the salt tolerance of tall fescue.

Genome-Wide Characterization of PIN Auxin Efflux Carrier Gene Family in Mikania micrantha

Mikania micrantha, recognized as one of the world's top 10 pernicious weeds, is a rapidly spreading tropical vine that has invaded the coastal areas of South China, causing serious economic losses and environmental damage. Rapid stem growth is an important feature of M. micrantha which may be related to its greater number of genes involved in auxin signaling and transport pathways and its ability to synthesize more auxin under adverse conditions to promote or maintain stem growth. Plant growth and development is closely connected to the regulation of endogenous hormones, especially the polar transport and asymmetric distribution of auxin. The PIN-FORMED (PIN) auxin efflux carrier gene family plays a key role in the polar transport of auxin and then regulates the growth of different plant tissues, which could indicate that the rapid growth of M. micrantha is closely related to this PIN-dependent auxin regulation. In this study, 11 PIN genes were identified and the phylogenetic relationship and structural compositions of the gene family in M. micrantha were analyzed by employing multiple bioinformatic methods. The phylogenetic analysis indicated that the PIN proteins could be divided into five distinct clades. The structural analysis revealed that three putative types of PIN (canonical, noncanonical and semi-canonical) exist among the proteins according to the length and the composition of the hydrophilic domain. The majority of the PINs were involved in the process of axillary bud differentiation and stem response under abiotic stress, indicating that M. micrantha may regulate its growth, development and stress response by regulating PIN expression in the axillary bud and stem, which may help explain its strong growth ability and environmental adaptability. Our study emphasized the structural features and stress response patterns of the PIN gene family and provided useful insights for further study into the molecular mechanism of auxin-regulated growth and control in M. micrantha.

Potassium ion regulates hormone, Ca2+ and H2O2 signal transduction and antioxidant activities to improve salt stress resistance in tobacco

Although improvement of plant salt tolerance by potassium ions (K+) has been widely studied, whether the tolerance is mediated via hormone signaling or antioxidant systems remains to be explored. This study combined plant physiology with transcriptomic techniques to study how K+ interacts with hormones and antioxidant enzymes to improve plant salt tolerance. Tobacco was used as the test material to study the effects of exogenous potassium application on photosynthetic function, hormone signal transduction, and reactive oxygen species (ROS) production under NaCl stress. The study also evaluated the function of the Ca2+ signaling pathway in salt stress tolerance. Transcriptome data showed that 4413 up-regulated genes and 3743 down-regulated genes were found in tobacco leaves treated with NaCl compared with the control. Compared with NaCl, the down-regulated genes in tobacco leaves were significantly reduced under NaCl + KCL treatment. The results showed that NaCl stress caused oxidative damage to tobacco leaves due to increased superoxide anion (O2-) content, superoxide dismutase (SOD) dismutates superoxide anion to produce hydrogen peroxide and the accumulation of H2O2 caused by reduced ascorbate peroxidase (APX) and peroxidase (POD) activities. NaCl stress also increased abscisic acid (ABA) content in tobacco leaves, resulting in stomatal closure and reduced photosynthetic capacity. Transcriptome data showed that 5 SOD, 1 POD, 1 CAT, 5 APX, and 3 GPX genes were significantly down-regulated by the NaCl treatment. Contrarily, NaCl + KCl treatment reduced the accumulation of O2-and SOD activity but increased POD activity, thereby reducing the accumulation of H2O2 and alleviating oxidative damage. The expression of 2 SOD and 3 APX and 2 GPX genes was significantly higher in NaCl + KCl treatment than that in NaCl treatment. Sufficient K+ also increased indole acetic acid (IAA) levels in tobacco leaves under NaCl stress but reduced ABA content, promoting stomatal opening and improving the photosynthetic capacity. In conclusion, K+ can improve plant salt tolerance by alleviating oxidative damage and regulating hormone signal transduction.

Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove (Sonneratia apetala Buch.-Ham.)

MicroRNAs (miRNAs) are small RNA molecules that serve as key players in plant stress responses. Although stress-regulated miRNAs have been explored in various plants, they are not well studied in mangroves. Herein, we combined PacBio isoform sequencing (Iso-Seq) with BGISEQ short-read RNA-seq to probe the role of miRNAs in the salt stress response of the mangrove plant, Sonneratia apetala Buch.-Ham. A total of 1,702,463 circular consensus sequencing reads were generated that produced 295,501 nonredundant full-length transcripts from the leaves of a 1-year-old S. apetala. After sequencing nine small RNA libraries constructed from control and 1- and 28-day 300 mM NaCl treatments, we identified 143 miRNAs (114 known and 29 novel) from a total of >261 million short reads. With the criteria of |log2FC| ≥ 1 and q-value < 0.05, 42 and 70 miRNAs were differentially accumulated after 1- and 28-day salt treatments, respectively. These differential accumulated miRNAs potentially targeted salt-responsive genes encoding transcription factors, ion homeostasis, osmotic protection, and detoxificant-related proteins, reminiscent of their responsibility for salinity adaptation in S. apetala. Particularly, 62 miRNAs were Sonneratia specific under salt stress, of which 34 were co-expressed with their 131 predicted targets, thus producing 140 miRNA-target interactions. Of these, 82 miRNA-target pairs exhibited negative correlations. Eighteen miRNA targets were categorized for the 'environmental information processing' during KEGG analysis and were related to plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), and ABC transporters (ko02010). These results underscored miRNAs as possible contributors to mangrove success in severe environments and offer insights into an miRNA-mediated regulatory mechanism of salt response in S. apetala.

Auxin response factors in plant adaptation to drought and salinity stress

Salinity and drought stresses affect plant growth worldwide and limit crop production. Auxin is crucial in regulating plants' salinity and drought stress adaptative response. As a chemical messenger, auxin influences gene expression through a family of functionally distinct transcription factors, the DNA-binding AUXIN RESPONSE FACTORS (ARFs). Various studies have revealed the important roles of ARFs in regulating drought and salinity stress responses in plants. Different ARFs regulate soluble sugar content, promote root development, and maintain chlorophyll content under drought and saline stress conditions to help plants adapt to these stresses. The functional characterization of ARFs pertaining to the regulation of drought and salinity stress responses is still in its infancy. Interestingly, the small RNA-mediated post-transcriptional regulation of ARF expression has been shown to influence plant responses to both stresses. The current knowledge on the diverse roles of ARFs in conferring specificity to auxin-mediated drought and salinity stress responses has not been reviewed to date. In this review, we summarize the recent research concerning the role of ARFs in response to drought and salinity stresses: gene expression patterns, functional characterization, and post-transcriptional regulation under drought and salinity stresses. We have also reviewed the modulation of ARF expression by other molecular regulators in the context of drought and salt stress signaling.

Bacterial Modulation of the Plant Ethylene Signaling Pathway Improves Tolerance to Salt Stress in Lettuce (Lactuca sativa L.)

Salinity has extensive adverse effects on plant growth and the development of new agronomic strategies to improve crop salt tolerance is becoming necessary. Currently, the use of plant growth promoting rhizobacteria (PGPR) to mitigate abiotic stress in crops is of increasing interest. The most analyzed mechanism is based on ACC deaminase activity, an enzyme that decreases the ethylene synthesis, an important phytohormone in plant stress response. We aimed to identify other PGPR mediated mechanisms involved in the regulation of salt stress in plant. We used three PGPR strains (ESL001, ESL007, SH31), of which only ESL007 demonstrated ACC deaminase activity, to evaluate their effect on lettuce plants under salt stress (100 mM NaCl). We measured growth and biochemical parameters (e.g., proline content, lipid peroxidation and ROS degradation), as well as expression levels of genes involved in ethylene signaling (CTR1, EBF1) and transcription factors induced by ethylene (ERF5, ERF13). All bacterial strains enhanced growth on salt-stressed lettuce plants and modulated the proline levels. Strains ESL007 and SH31 triggered a higher catalase and ascorbate-peroxidase activity, compared to non-stressed plants. Differential expression of ethylene-related genes in inoculated plants subjected to salinity was observed. We gained consistent evidence for the existence of alternative mechanisms to ethylene modulation, which probably rely on bacterial IAA production and other chemical signals. These mechanisms modify the expression of genes associated with ethylene signaling and regulation, complementarily to the ACC deaminase model to diminish abiotic stress responses.

The Tiny Companion Matters: The Important Role of Protons in Active Transports in Plants

In plants, the translocation of molecules, such as ions, metabolites, and hormones, between different subcellular compartments or different cells is achieved by transmembrane transporters, which play important roles in growth, development, and adaptation to the environment. To facilitate transport in a specific direction, active transporters that can translocate their substrates against the concentration gradient are needed. Examples of major active transporters in plants include ATP-binding cassette (ABC) transporters, multidrug and toxic compound extrusion (MATE) transporters, monosaccharide transporters (MSTs), sucrose transporters (SUTs), and amino acid transporters. Transport via ABC transporters is driven by ATP. The electrochemical gradient across the membrane energizes these secondary transporters. The pH in each cell and subcellular compartment is tightly regulated and yet highly dynamic, especially when under stress. Here, the effects of cellular and subcellular pH on the activities of ABC transporters, MATE transporters, MSTs, SUTs, and amino acid transporters will be discussed to enhance our understanding of their mechanics. The relation of the altered transporter activities to various biological processes of plants will also be addressed. Although most molecular transport research has focused on the substrate, the role of protons, the tiny counterparts of the substrate, should also not be ignored.

Small RNA and Degradome Sequencing Reveal Important MicroRNA Function in Nicotiana tabacum Response to Bemisia tabaci

MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, are key molecules in many biological and metabolic processes of plant growth, development and stress response via targeting mRNAs. The phloem-feeding insect whitefly Bemisia tabaci (Hemiptera, Aleyrodidae) is a serious pest that causes devastating harm to agricultural production worldwide. However, the function of host miRNAs in the response to whitefly infestation remains unclear. Here, we sequenced the small RNA and degradome of tobacco (Nicotiana tabacum L.), after and before infestation by B. tabaci. We identified 1291 miRNAs belonging to 138 miRNA families including 706 known miRNAs and 585 novel miRNAs. A total of 47 miRNAs were differentially expressed, of which 30 were upregulated and 17 were downregulated by whitefly exposure. Then, computational analysis showed that the target genes of differential miRNAs were involved in R gene regulation, plant innate immunity, plant pathogen defense, the plant hormone signal pathway and abiotic stress tolerance. Furthermore, degradome analysis demonstrated that 253 mRNAs were cleaved by 66 miRNAs. Among them, the targets cleaved by upregulated miR6025, miR160, miR171, miR166 and miR168 are consistent with our prediction, suggesting that pathogen-related miRNAs may function in plant defense against whitefly. Moreover, our results show that plant miRNA response and miRNA-mediated post-transcriptional regulation for phloem-feeding insect infestation are similar to pathogen invasion. Our study provides additional data to further elucidate how host plants respond and defend the phloem-feeding insects.

A novel mitochondrial protein is required for cell wall integrity, auxin accumulation and root elongation in Arabidopsis under salt stress

Maintenance of root elongation is beneficial for the growth and survival of plants under salt stress, but currently the cellular components involved in the regulation of root growth under high salinity are not fully understood. In this study, we identified an Arabidopsis mutant, rres1, which exhibited reduced root elongation under treatment of a variety of salts, including NaCl, NaNO3, KCl, and KNO3. RRES1 encodes a novel mitochondrial protein and its molecular function is still unknown. Under salt stress, the root meristem length was shorter in the rres1 mutant compared to the wild type, which was correlated with a reduced auxin accumulation in the mutant. Reactive oxygen species (ROS), as important signals that regulate root elongation, were accumulated to higher levels in the rres1 mutant than the wild type after salt treatment. Measurement of monosaccharides in the cell wall showed that arabinose and xylose contents were decreased in the rres1 mutant under salt stress, and application of boric acid, which is required for the crosslinking of pectic polysaccharide rhamnogalacturonan-II (RG-II), largely rescued the root growth arrest of the rres1 mutant, suggesting that RRES1 participates in the maintenance of cell wall integrity under salt stress. GUS staining assay indicated that the RRES1 gene was expressed in leaves and weakly in root tip under normal conditions, but its expression was dramatically increased in leaves and roots after salt treatment. Together, our study reveals a novel mitochondrial protein that regulates root elongation under salt stress via the modulation of cell wall integrity, auxin accumulation, and ROS homeostasis.

Integrated de novo Analysis of Transcriptional and Metabolic Variations in Salt-Treated Solenostemma argel Desert Plants

Solenostemma argel (Delile) Hayne is a desert plant that survives harsh environmental conditions with several vital medicinal properties. Salt stress is a major constraint limiting agricultural production around the globe. However, response mechanisms behind the adaptation of S. argel plants to salt stress are still poorly understood. In the current study, we applied an omics approach to explore how this plant adapts to salt stress by integrating transcriptomic and metabolomic changes in the roots and leaves of S. argel plants under salt stress. De novo assembly of transcriptome produced 57,796 unigenes represented by 165,147 transcripts/isoforms. A total of 730 differentially expressed genes (DEGs) were identified in the roots (396 and 334 were up- and down-regulated, respectively). In the leaves, 927 DEGs were identified (601 and 326 were up- and down-regulated, respectively). Gene ontology and Kyoto Encyclopedia of Genes And Genomes pathway enrichment analyses revealed that several defense-related biological processes, such as response to osmotic and oxidative stress, hormonal signal transduction, mitogen-activated protein kinase signaling, and phenylpropanoid biosynthesis pathways are the potential mechanisms involved in the tolerance of S. argel plants to salt stress. Furthermore, liquid chromatography-tandem mass spectrometry was used to detect the metabolic variations of the leaves and roots of S. argel under control and salt stress. 45 and 56 critical metabolites showed changes in their levels in the stressed roots and leaves, respectively; there were 20 metabolites in common between the roots and leaves. Differentially accumulated metabolites included amino acids, polyamines, hydroxycinnamic acids, monolignols, flavonoids, and saccharides that improve antioxidant ability and osmotic adjustment of S. argel plants under salt stress. The results present insights into potential salt response mechanisms in S. argel desert plants and increase the knowledge in order to generate more tolerant crops to salt stress.

Phospholipids in Salt Stress Response

High salinity threatens crop production by harming plants and interfering with their development. Plant cells respond to salt stress in various ways, all of which involve multiple components such as proteins, peptides, lipids, sugars, and phytohormones. Phospholipids, important components of bio-membranes, are small amphoteric molecular compounds. These have attracted significant attention in recent years due to the regulatory effect they have on cellular activity. Over the past few decades, genetic and biochemical analyses have partly revealed that phospholipids regulate salt stress response by participating in salt stress signal transduction. In this review, we summarize the generation and metabolism of phospholipid phosphatidic acid (PA), phosphoinositides (PIs), phosphatidylserine (PS), phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), as well as the regulatory role each phospholipid plays in the salt stress response. We also discuss the possible regulatory role based on how they act during other cellular activities.

Potassium: A track to develop salinity tolerant plants

Salinity is one of the major constraints to plant growth and development across the globe that leads to the huge crop productivity loss. Salinity stress causes impairment in plant's metabolic and cellular processes including disruption in ionic homeostasis due to excess of sodium (Na⁺) ion influx and potassium (K⁺) efflux. This condition subsequently results in a significant reduction of the cytosolic K⁺ levels, eventually inhibiting plant growth attributes. K⁺ plays a crucial role in alleviating salinity stress by recasting key processes of plants. In addition, K⁺ acquisition and retention also serve as the perquisite trait to establish salt tolerant mechanism. In addition, an intricate network of genes and their regulatory elements are involved in coordinating salinity stress responses. Furthermore, plant growth regulators (PGRs) and other signalling molecules influence K⁺-mediated salinity tolerance in plants. Recently, nanoparticles (NPs) have also been found several implications in plants with respect to their roles in mediating K⁺ homoeostasis during salinity stress in plants. The present review describes salinity-induced adversities in plants and role of K⁺ in mitigating salinity-induced damages. The review also highlights the efficacy of PGRs and other signalling molecules in regulating K⁺ mediated salinity tolerance along with nano-technological perspective for improving K⁺ mediated salinity tolerance in plants.

Jute Responses and Tolerance to Abiotic Stress: Mechanisms and Approaches

Jute (Corchorus spp.) belongs to the Malvaceae family, and there are two species of jute, C. capsularis and C. olitorious. It is the second-largest natural bast fiber in the world according to production, which has diverse uses not only as a fiber but also as multiple industrial materials. Because of climate change, plants experience various stressors such as salt, drought, heat, cold, metal/metalloid toxicity, and flooding. Although jute is particularly adapted to grow in hot and humid climates, it is grown under a wide variety of climatic conditions and is relatively tolerant to some environmental adversities. However, abiotic stress often restricts its growth, yield, and quality significantly. Abiotic stress negatively affects the metabolic activities, growth, physiology, and fiber yield of jute. One of the major consequences of abiotic stress on the jute plant is the generation of reactive oxygen species, which lead to oxidative stress that damages its cellular organelles and biomolecules. However, jute’s responses to abiotic stress mainly depend on the plant’s age and type and duration of stress. Therefore, understanding the abiotic stress responses and the tolerance mechanism would help plant biologists and agronomists in developing climate-smart jute varieties and suitable cultivation packages for adverse environmental conditions. In this review, we summarized the best possible recent literature on the plant abiotic stress factors and their influence on jute plants. We described the possible approaches for stress tolerance mechanisms based on the available literature.

Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress

Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress.

Analysis of Phytohormone Signal Transduction in Sophora alopecuroides under Salt Stress

Salt stress seriously restricts crop yield and quality, leading to an urgent need to understand its effects on plants and the mechanism of plant responses. Although phytohormones are crucial for plant responses to salt stress, the role of phytohormone signal transduction in the salt stress responses of stress-resistant species such as Sophora alopecuroides has not been reported. Herein, we combined transcriptome and metabolome analyses to evaluate expression changes of key genes and metabolites associated with plant hormone signal transduction in S. alopecuroides roots under salt stress for 0 h to 72 h. Auxin, cytokinin, brassinosteroid, and gibberellin signals were predominantly involved in regulating S. alopecuroides growth and recovery under salt stress. Ethylene and jasmonic acid signals may negatively regulate the response of S. alopecuroides to salt stress. Abscisic acid and salicylic acid are significantly upregulated under salt stress, and their signals may positively regulate the plant response to salt stress. Additionally, salicylic acid (SA) might regulate the balance between plant growth and resistance by preventing reduction in growth-promoting hormones and maintaining high levels of abscisic acid (ABA). This study provides insight into the mechanism of salt stress response in S. alopecuroides and the corresponding role of plant hormones, which is beneficial for crop resistance breeding.

The Diverse Salt-Stress Response of Arabidopsis ctr1-1 and ein2-1Ethylene Signaling Mutants Is Linked to Altered Root Auxin Homeostasis

We explored the interplay between ethylene signals and the auxin pool in roots exposed to high salinity using Arabidopsisthaliana wild-type plants (Col-0), and the ethylene-signaling mutants ctr1-1 (constitutive) and ein2-1 (insensitive). The negative effect of salt stress was less pronounced in ctr1-1 individuals, which was concomitant with augmented auxin signaling both in the ctr1-1 controls and after 100 mM NaCl treatment. The R2D2 auxin sensorallowed mapping this active auxin increase to the root epidermal cells in the late Cell Division (CDZ) and Transition Zone (TZ). In contrast, the ethylene-insensitive ein2-1 plants appeared depleted in active auxins. The involvement of ethylene/auxin crosstalk in the salt stress response was evaluated by introducing auxin reporters for local biosynthesis (pTAR2::GUS) and polar transport (pLAX3::GUS, pAUX1::AUX1-YFP, pPIN1::PIN1-GFP, pPIN2::PIN2-GFP, pPIN3::GUS) in the mutants. The constantly operating ethylene-signaling pathway in ctr1-1 was linked to increased auxin biosynthesis. This was accompanied by a steady expression of the auxin transporters evaluated by qRT-PCR and crosses with the auxin transport reporters. The results imply that the ability of ctr1-1 mutant to tolerate high salinity could be related to the altered ethylene/auxin regulatory loop manifested by a stabilized local auxin biosynthesis and transport.

Simultaneous Biochemical and Physiological Responses of the Roots and Leaves of Pancratium maritimum (Amaryllidaceae) to Mild Salt Stress

Pancratium maritimum (Amaryllidaceae) is a bulbous geophyte growing on coastal sands. In this study, we investigated changes in concentrations of metabolites in the root and leaf tissue of P. maritimum in response to mild salt stress. Changes in concentrations of osmolytes, glutathione, sodium, mineral nutrients, enzymes, and other compounds in the leaves and roots were measured at 0, 3, and 10 days during a 10-day exposure to two levels of mild salt stress, 50 mM NaCl or 100 mM NaCl in sandy soil from where the plants were collected in dunes near Cuma, Italy. Sodium accumulated in the roots, and relatively little was translocated to the leaves. At both concentrations of NaCl, higher values of the concentrations of oxidized glutathione disulfide (GSSG), compared to reduced glutathione (GSH), in roots and leaves were associated with salt tolerance. The concentration of proline increased more in the leaves than in the roots, and glycine betaine increased in both roots and leaves. Differences in the accumulation of organic osmolytes and electron donors synthesized in both leaves and roots demonstrate that osmoregulatory and electrical responses occur in these organs of P. maritimum under mild salt stress.

Abiotic Stress in Crop Species: Improving Tolerance by Applying Plant Metabolites

Reductions in crop yields brought about by abiotic stress are expected to increase as climate change, and other factors, generate harsher environmental conditions in regions traditionally used for cultivation. Although breeding and genetically modified and edited organisms have generated many varieties with greater abiotic stress tolerance, their practical use depends on lengthy processes, such as biological cycles and legal aspects. On the other hand, a non-genetic approach to improve crop yield in stress conditions involves the exogenous application of natural compounds, including plant metabolites. In this review, we examine the recent literature related to the application of different natural primary (proline, l-tryptophan, glutathione, and citric acid) and secondary (polyols, ascorbic acid, lipoic acid, glycine betaine, α-tocopherol, and melatonin) plant metabolites in improving tolerance to abiotic stress. We focus on drought, saline, heavy metal, and temperature as environmental parameters that are forecast to become more extreme or frequent as the climate continues to alter. The benefits of such applications are often evaluated by measuring their effects on metabolic, biochemical, and morphological parameters in a variety of crop plants, which usually result in improved yields when applied in greenhouse conditions or in the field. As this strategy has proven to be an effective way to raise plant tolerance to abiotic stress, we also discuss the prospect of its widespread implementation in the short term.

Overexpression of the Auxin Receptor AFB3 in Arabidopsis Results in Salt Stress Resistance and the Modulation of NAC4 and SZF1

Soil salinity is a key problem for crop production worldwide. High salt concentration in soil negatively modulates plant growth and development. In roots, salinity affects the growth and development of both primary and lateral roots. The phytohormone auxin regulates various developmental processes during the plant’s life cycle, including several aspects of root architecture. Auxin signaling involves the perception by specialized receptors which module several regulatory pathways. Despite their redundancy, previous studies have shown that their functions can also be context-specific depending on tissue, developmental or environmental cues. Here we show that the over-expression of Auxin Signaling F-Box 3 receptor results in an increased resistance to salinity in terms of root architecture and germination. We also studied possible downstream signaling components to further characterize the role of auxin in response to salt stress. We identify the transcription factor SZF1 as a key component in auxin-dependent salt stress response through the regulation of NAC4. These results give lights of an auxin-dependent mechanism that leads to the modulation of root system architecture in response to salt identifying a hormonal cascade important for stress response.

Role of Arabidopsis RAB5 GEF vps9a in maintaining potassium levels under sodium chloride stress

Salt stress is one of the major factors impacting crop productivity worldwide. Through a variety of effector and signaling pathways, plants achieve survival under salinity stress by maintaining high cytosolic potassium/sodium ion (K+/Na+) ratios, preventing Na+ cytotoxicity, and retaining osmotic balance. Ras-related protein 5 (Rab5) members are involved in the trafficking of endosomes to the vacuole or plasma membrane (PM). The vacuolar protein sorting- associated protein 9 (vps9a) encodes the single guanine nucleotide exchange factor (GEF) that activates all three known Rab5 proteins in Arabidopsis thaliana. Previous work from our group has reported the critical function of vps9a for the operation of salt-induced endocytic pathway, as well as the expansion of endomembrane compartments under saline stress conditions. Here we show an additional role of vps9a in plant response to salt stress via maintenance of K+ status of the cell rather than Na+ homeostasis. Our results show that roots from vps9a-2 mutant, subjected to 100 mM NaCl, display alterations in transcript levels of genes involved in the K+ homeostasis pathway. Concurrent with the observed sensitivity of vps9a-2 mutant under NaCl stress, exposure to low K+ environments resulted in growth retardation, and reduced rate of endocytosis. Furthermore, vps9a-2 mutant displays reduced expression of auxin reporter, Direct Repeat-5 (DR5), and alterations in polarity and abundance of auxin efflux carrier PIN- FORMED2 (PIN2). Imposition of NaCl stress was found to be restrictive to the elongation capacity of cells in the root elongation zone of vps9a-2 mutant. Together our results indicate that alterations in K+ homeostasis and associated cellular changes causing increased cell wall pH, contribute to diminished root growth and compromised survival of vps9a-2 mutant under salt stress conditions.

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

Watermelon (Citrullus lanatus L.) is a widely popular vegetable fruit crop for human consumption. Soil salinity is among the most critical problems for agricultural production, food security, and sustainability. The transcriptomic and the primary molecular mechanisms that underlie the salt-induced responses in watermelon plants remain uncertain. In this study, the photosynthetic efficiency of photosystem II, free amino acids, and transcriptome profiles of watermelon seedlings exposed to short-term salt stress (300 mM NaCl) were analyzed to identify the genes and pathways associated with response to salt stress. We observed that the maximal photochemical efficiency of photosystem II decreased in salt-stressed plants. Most free amino acids in the leaves of salt-stressed plants increased many folds, while the percent distribution of glutamate and glutamine relative to the amino acid pool decreased. Transcriptome analysis revealed 7622 differentially expressed genes (DEGs) under salt stress, of which 4055 were up-regulated. The GO analysis showed that the molecular function term “transcription factor (TF) activity” was enriched. The assembled transcriptome demonstrated up-regulation of 240 and down-regulation of 194 differentially expressed TFs, of which the members of ERF, WRKY, NAC bHLH, and MYB-related families were over-represented. The functional significance of DEGs associated with endocytosis, amino acid metabolism, nitrogen metabolism, photosynthesis, and hormonal pathways in response to salt stress are discussed. The findings from this study provide novel insights into the salt tolerance mechanism in watermelon.