Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure

Succinic acid synthesis regulated by succinyl-coenzyme A ligase (SUCLA) plays an important role in root response to alkaline salt stress in Leymus chinensis

Alkaline salts have more severe adverse effects on plant growth and development than neutral salts do. However, the adaptive mechanisms of plants to alkaline salt stress remain poorly understood, especially at the molecular level. The Songnen Plain in northeast China is composed of typical 'soda' saline-alkali soil, with NaHCO3 and Na2CO3 as the predominant alkaline salts (pH ≥ 9.2). Leymus chinensis can grow on this saline-alkali land, showing strong adaptability. We investigated the role of succinic acid and genes regulating its synthesis in the response to alkaline salt stress in L. chinensis roots. Compared to the neutral salt (NaCl) and high pH treatments, the alkaline salt (NaHCO3 and Na2CO3) treatment specifically caused changes in 11 organic acids, of which the increase in succinic acid was the greatest. The exogenous addition of succinic acid alleviates the damage of alkaline salt to L. chinensis roots. Further, two genes encoding succinyl-coenzyme A ligase (SUCLA) subunits that regulate succinic acid synthesis, LcSUCLAα and LcSUCLAβ, were identified; these genes interact and were localized within mitochondria. Overexpression of LcSUCLAα and LcSUCLAβ caused an increase in succinic acid and enhanced tolerance of NaHCO3 in transgenic rice seedlings. These results suggest that LcSUCLAα and LcSUCLAβ may be involved in the response to alkaline salt stress through the regulation of succinic acid synthesis.

Growing on calcareous soils and facing climate change

Soil calcium carbonate (CaCO3) impacts plant mineral nutrition far beyond Fe metabolism, imposing constraints for crop growth and quality in calcareous agrosystems. Our knowledge on plant strategies to tolerate CaCO3 effects mainly refers to Fe acquisition. This review provides an update on plant cellular and molecular mechanisms recently described to counteract the negative effects of CaCO3 in soils, as well as recent efforts to identify genetic bases involved in CaCO3 tolerance from natural populations, that could be exploited to breed CaCO3-tolerant crops. Finally, we review the impact of environmental factors (soil water content, air CO2, and temperature) affecting soil CaCO3 equilibrium and plant tolerance to calcareous soils, and we propose strategies for improvement in the context of climate change.

A role for root carbonic anhydrase βCA4 in the bicarbonate tolerance of Arabidopsis thaliana

Carbonic anhydrases (CAs) are the main enzymes handling bicarbonate in the different cell compartments. This study analyses the expression of CAs in roots of Arabidopsis thaliana demes differing in tolerance to bicarbonate: the tolerant A1(C+) deme and the sensitive deme, T6(C-). Exposure to 10 mM NaCl caused a transient depolarization of the root cell membranes, and in contrast, the supply of 10 mM NaHCO3 caused hyperpolarization. This hyperpolarization was much stronger in A1(C+) than in T6(C-). Acetazolamide (AZ), a specific inhibitor of CAs, abolished the hyperpolarizing effect in A1(C+), indicating the implication of CAs in this fast membrane response. The time-dependent (3 to 72 h) expression profiles of 14 CAs in roots of A1(C+) and T6(C-) exposed to either control (0 mM NaHCO3, pH 5.9), or bicarbonate (10 mM NaHCO3,pH 8.3) conditions revealed a bicarbonate specific upregulation of BCA4.1 (from 3 to 12 h) in A1(C+). Contrastingly, in T6(C-) BCA4.1 was downregulated by NaHCO3. Exclusively in A1(C+), the enhanced expression of BCA4.1 under bicarbonate was parallelled by an increase of PIP1,3, SLAH1, SLAH3, AHA2, and FRO2 gene expression levels. Under HCO3 - exposure, a bca4 knockout mutant had a lower number of lateral roots, lower root diameters, and higher root lipid peroxidation than the WT. These results indicate that bicarbonate-induced root membrane hyperpolarization is the fast (minutes) initial signalling event in the tolerance response. This is followed by the specific upregulation of BCA4.1 and genes involved in H2O and CO2 transport, apoplast acidification, and iron acquisition.

Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa

Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1' was treated with 50 mM NaHCO3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties.

Root-based inorganic carbon uptake increases the growth of Arabidopsis thaliana and changes transporter expression and nitrogen and sulfur metabolism

Root-based uptake of inorganic carbon has been suggested as an additional carbon source. Our study aimed to characterize and understand the root-based uptake and fixation mechanisms and their impact on plant growth. 13C-labeled bicarbonate fed to Arabidopsis roots was assimilated into aspartic acid but mainly into sucrose, indicating that the added inorganic carbon was transported to the leaves. A hydroponic treatment was also established for A. thaliana using 2 mM NaHCO3 at pH 5.6, which enhanced the photosynthetic and growth parameters. According to transcriptome sequencing data, the observed enhancement in growth may be orchestrated by trehalose-6-phosphate signaling and supported by augmented nitrogen and sulfur assimilation. The analysis also revealed regulatory and transporter activities, including several nitrate (NRT2.1), and sulfate transporter (SULTR1;1 and SULTR1;2) candidates that could participate in bicarbonate uptake. Different transporters and carbon fixation mutants were assessed. Arabidopsis homologs of SLOW-TYPE ANION CHANNEL 1 (slah3) CARBONIC ANHYDRASE (βca4), and SULFATE TRANSPORTER (sultr1;2) mutants were shown to be inferior to the bicarbonate-treated wild types in several growth and root ultrastructural parameters. Besides, aquaporin genes PIP1;3 and PIP2;6 could play a negative role in the carbon uptake by venting carbon dioxide out of the plant. The findings support the hypothesis that the inorganic carbon is taken up by the root anion channels, mostly transported up to the shoots by the xylem, and fixed there by RuBisCo after the conversion to CO2 by carbonic anhydrases. The process boosts photosynthesis and growth by providing an extra carbon supply.

Establishment and Maintenance of Heat-Stress Memory in Plants

Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for maintaining heat-stress memory. The chromatin opening state is influenced by epigenetic modifications, making DNA and histone modifications important entry points for understanding heat-shock memory. Current research suggests that traditional heat-stress signaling pathway components might be involved in chromatin opening, thereby promoting the establishment of heat-stress memory in plants. In this review, we discuss the relationship between chromatin structure-based maintenance and the establishment of heat-stress memory. We also discuss the association between traditional heat-stress signals and epigenetic modifications. Finally, we discuss potential research ideas for exploring plant adaptation to high-temperature stress in the future.

Combined genomics to discover genes associated with tolerance to soil carbonate

Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1(c+) and T6(c - ) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO3 , pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1(c+) and T6(c - ) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1(c+) versus T6(c - ) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1(c+) and T6(c - ) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.

Magnetic Iron-Improved Growth, Leaf Chemical Content, Yield, and Fruit Quality of Chinese Mandarin Trees Grown under Soil Salinity Stress

Chinese mandarin fruits are an inexpensive and rich source of vitamin C. They have potential benefits in treating acute respiratory infections and mitigating inflammation in critical patients with COVID-19. In Egypt, citrus is the most important fruit tree but is sensitive to salinity stress, resulting in poor vegetative tree growth and reductions in productivity and fruit quality. Magnetic iron has emerged as a promising approach in the citrus tree industry, since it improves vegetative growth, yield, and fruit quality and alleviates salinity stress in Chinese mandarin trees grown in soils suffering from high salt stress. This research is aimed at studying the influence of adding magnetic iron (as soil treatment) on tree canopy growth, yield, and fruit quality of 'Chinese' mandarin trees. Therefore, the treatments were as follows: 0, 250, 500, and or 750 g of magnetic iron.tree^-1. Our results indicated that all applications of magnetic iron significantly improved tree canopy volume, leaf total chlorophyll, relative water content, yield (kg.tree^-1), and the fruit physical and chemical characteristics of Chinese mandarin. In contrast, leaf Na and Cl content, (%), proline, and total phenolic content were decreased by magnetic iron soil treatments. In respect to vegetative growth, our results indicated that adding magnetic iron at the concentration 750 g.tree^-1 caused the best values of tree canopy volume. A similar trend was noticed regarding yield. The increase in yield attained was nearly 19%; the best values were obtained when magnetic iron were used at 750 g.tree^-1. In conclusion, the application of magnetic iron can lead to improved fruit production and fruit quality of Chinese mandarin trees grown in salinity stress conditions.

Alkali salt stress causes fast leaf apoplastic alkalinization together with shifts in ion and metabolite composition and transcription of key genes during the early adaptive response of Vicia faba L

The mechanisms by which plants respond to alkali salt stress are still obscure, and the relevance of alkaline pH under combined alkali salt stress. Early stress responses can indicate mechanisms leading to damage and plant resistance. The apoplast contains essential determinants for plant growth, specifically early apoplastic pH fluctuations are induced by many stressors and hypothesized to be involved in stress signalling. Hence, this study aims to identify fast responses specific to alkaline pH and alkali salt stress by exposing the root of hydroponically grown Vicia faba L. plants to 150 min of either 50 mM NaHCO₃ (pH 9) treatment or alkaline pH 9 alone. Apoplastic pH was monitored in real-time by ratiometric fluorescence microscopy simultaneously with SWIR transmission-based measurements of leaf water content (LWC). Moreover, we examined the effect of these stresses on apoplastic, symplastic and xylem ion and metabolite composition together with transcriptions of certain stress-responsive genes. Physiological and transcriptional changes were observed in response to NaHCO₃ but not to alkaline pH alone. NaHCO₃ elicited a transient reduction in LWC, followed by a transient alkalinization of the apoplast and stomatal closure. Simultaneously, organic acids and sugars accumulated. Fast upregulation of stress-responsive genes showed the significance of gene regulation for early plant adaptation to alkali salt stress.

Environmental Stress and Plants

Land plants are constantly subjected to multiple unfavorable or even adverse environmental conditions. Among them, abiotic stresses (such as salt, drought, heat, cold, heavy metals, ozone, UV radiation, and nutrient deficiencies) have detrimental effects on plant growth and productivity and are increasingly important considering the direct or indirect effects of climate change. Plants respond in many ways to abiotic stresses, from gene expression to physiology, from plant architecture to primary, and secondary metabolism. These complex changes allow plants to tolerate and/or adapt to adverse conditions. The complexity of plant response can be further influenced by the duration and intensity of stress, the plant genotype, the combination of different stresses, the exposed tissue and cell type, and the developmental stage at which plants perceive the stress. It is therefore important to understand more about how plants perceive stress conditions and how they respond and adapt (both in natural and anthropogenic environments). These concepts were the basis of the Special Issue that International Journal of Molecular Sciences expressly addressed to the relationship between environmental stresses and plants and that resulted in the publication of 5 reviews and 38 original research articles. The large participation of several authors and the good number of contributions testifies to the considerable interest that the topic currently receives in the plant science community, especially in the light of the foreseeable climate changes. Here, we briefly summarize the contributions included in the Special Issue, both original articles categorized by stress type and reviews that discuss more comprehensive responses to various stresses.

Identification of ARF family in blueberry and its potential involvement of fruit development and pH stress response

Background

Auxin responsive factor (ARF) family is one of core components in auxin signalling pathway, which governs diverse developmental processes and stress responses. Blueberry is an economically important berry-bearing crop and prefers to acidic soil. However, the understandings of ARF family has not yet been reported in blueberry.

Results

In the present study, 60 ARF genes (VcARF) were identified in blueberry, and they showed diverse gene structures and motif compositions among the groups and similar within each group in the phylogenetic tree. Noticeably, 9 digenic, 5 trigenic and 6 tetragenic VcARF pairs exhibited more than 95% identity to each other. Computational analysis indicated that 23 VcARFs harbored the miRNA responsive element (MRE) of miR160 or miR167 like other plant ARF genes. Interestingly, the MRE of miR156d/h-3p was observed in the 5’UTR of 3 VcARFs, suggesting a potentially novel post-transcriptional control. Furthermore, the transcript accumulations of VcARFs were investigated during fruit development, and three categories of transcript profiles were observed, implying different functional roles. Meanwhile, the expressions of VcARFs to different pH conditions (pH4.5 and pH6.5) were surveyed in pH-sensitive and tolerant blueberry species, and a number of VcARFs showed different transcript accumulations. More importantly, distinct transcriptional response to pH stress (pH6.5) were observed for several VcARFs (such as VcARF6s and VcARF19-3/19–4) between pH-sensitive and tolerant species, suggesting their potential roles in adaption to pH stress.

Conclusions

Sixty VcARF genes were identified and characterized, and their transcript profiles were surveyed during fruit development and in response to pH stress. These findings will contribute to future research for eliciting the functional roles of VcARFs and regulatory mechanisms, especially fruit development and adaption to pH stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08556-y.