Physiological and Transcriptome Responses to Combinations of Elevated CO2 and Magnesium in Arabidopsis thaliana

Comparative Physio-Biochemical and Transcriptome Analyses Reveal Contrasting Responses to Magnesium Imbalances in Leaves of Mulberry (Morus alba L.) Plants

Magnesium (Mg) deficiency is a major factor limiting the growth and development of plants. Mulberry (Morus alba L.) is an important fruit tree crop that requires Mg for optimal growth and yield, especially in acid soils. However, the molecular mechanism of Mg stress tolerance in mulberry plants remains unknown. In this study, we used next-generation sequencing technology and biochemical analysis to profile the transcriptome and physiological changes of mulberry leaves under different Mg treatments (deficiency: 0 mM, low: 1 mM, moderate low: 2 mM, sufficiency: 3 mM, toxicity: 6 mM, higher toxicity: 9 mM) as T1, T2, T3, CK, T4, T5 treatments, respectively, for 20 days. The results showed that Mg imbalance altered the antioxidant enzymatic activities, such as catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), and non-enzymatic, including soluble protein, soluble sugar, malondialdehyde (MDA), and proline (PRO), contents of the plant. The Mg imbalances disrupted the ultrastructures of the vital components of chloroplast and mitochondria relative to the control. The transcriptome data reveal that 11,030 genes were differentially expressed (DEGs). Genes related to the photosynthetic processes (CAB40, CAB7, CAB6A, CAB-151, CAP10A) and chlorophyll degradation (PAO, CHLASE1, SGR) were altered. Antioxidant genes such as PER42, PER21, and PER47 were downregulated, but DFR was upregulated. The carbohydrate metabolism pathway was significantly altered, while those involved in energy metabolism processes were perturbed under high Mg treatment compared with control. We also identified several candidate genes associated with magnesium homeostasis via RT-qPCR validation analysis, which provided valuable information for further functional characterization studies such as promoter activity assay or gene overexpression experiments using transient expression systems.

Progress in Salicylic Acid-Dependent Signaling for Growth–Defense Trade-Off

One grand challenge for studying plant biotic and abiotic stress responses is to optimize plant growth and plasticity under variable environmental constraints, which in the long run benefits agricultural production. However, efforts in promoting plant immunity are often accompanied by compromised morphological “syndromes” such as growth retardation, sterility, and reduced yield. Such a trade-off is dictated by complex signaling driven by secondary messengers and phytohormones. Salicylic acid (SA) is a well-known phytohormone essential for basal immunity and systemic acquired resistance. Interestingly, recent updates suggest that external environmental cues, nutrient status, developmental stages, primary metabolism, and breeding strategies attribute an additional layer of control over SA-dependent signaling, and, hence, plant performance against pathogens. In this review, these external and internal factors are summarized, focusing on their specific roles on SA biosynthesis and downstream signaling leading to immunity. A few considerations and future opportunities are highlighted to improve plant fitness with minimal growth compensation.

Short Term Elevated CO2 Interacts with Iron Deficiency, Further Repressing Growth, Photosynthesis and Mineral Accumulation in Soybean (Glycine max L.) and Common Bean (Phaseolus vulgaris L.)

Elevated CO2 (eCO2) has been reported to cause mineral losses in several important food crops such as soybean (Glycine max L.) and common bean (Phaseolus vulgaris L.). In addition, more than 30% of the world’s arable land is calcareous, leading to iron (Fe) deficiency chlorosis and lower Fe levels in plant tissues. We hypothesize that there will be combinatorial effects of eCO2 and Fe deficiency on the mineral dynamics of these crops at a morphological, biochemical and physiological level. To test this hypothesis, plants were grown hydroponically under Fe sufficiency (20 μM Fe-EDDHA) or deficiency (0 μM Fe-EDDHA) at ambient CO2 (aCO2, 400 ppm) or eCO2 (800 ppm). Plants of both species exposed to eCO2 and Fe deficiency showed the lowest biomass accumulation and the lowest root: shoot ratio. Soybean at eCO2 had significantly higher chlorophyll levels (81%, p < 0.0001) and common bean had significantly higher photosynthetic rates (60%, p < 0.05) but only under Fe sufficiency. In addition, eCO2 increased ferric chelate reductase acivity (FCR) in Fe-sufficient soybean by 4-fold (p < 0.1) and in Fe-deficient common bean plants by 10-fold (p < 0.0001). In common bean, an interactive effect of both environmental factors was observed, resulting in the lowest root Fe levels. The lowering of Fe accumulation in both crops under eCO2 may be linked to the low root citrate accumulation in these plants when grown with unrestricted Fe supply. No changes were observed for malate in soybean, but in common bean, shoot levels were significantly lower under Fe deficiency (77%, p < 0.05) and Fe sufficiency (98%, p < 0.001). These results suggest that the mechanisms involved in reduced Fe accumulation caused by eCO2 and Fe deficiency may not be independent, and an interaction of these factors may lead to further reduced Fe levels.

Automatic Stomatal Segmentation Based on Delaunay-Rayleigh Frequency Distance

The CO₂ and water vapor exchange between leaf and atmosphere are relevant for plant physiology. This process is done through the stomata. These structures are fundamental in the study of plants since their properties are linked to the evolutionary process of the plant, as well as its environmental and phytohormonal conditions. Stomatal detection is a complex task due to the noise and morphology of the microscopic images. Although in recent years segmentation algorithms have been developed that automate this process, they all use techniques that explore chromatic characteristics. This research explores a unique feature in plants, which corresponds to the stomatal spatial distribution within the leaf structure. Unlike segmentation techniques based on deep learning tools, we emphasize the search for an optimal threshold level, so that a high percentage of stomata can be detected, independent of the size and shape of the stomata. This last feature has not been reported in the literature, except for those results of geometric structure formation in the salt formation and other biological formations.

Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana

Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented the identification and characterization of lncRNAs under seven nutrient stress conditions. The expression pattern analysis revealed that aberrant expression of lncRNAs is a stress-specific manner under nutrient stress conditions and that lncRNAs are more sensitive to nutrient stress than protein-coding genes (PCGs). Moreover, competing endogenous RNA (ceRNA) network and lncRNA-mRNA co-expression network (CEN) were constructed to explore the potential function of these lncRNAs under nutrient stress conditions. We further combined different expressed lncRNAs with ceRNA network and CEN to select key lncRNAs in response to nutrient stress. Together, our study provides important information for further insights into the role of lncRNAs in response to stress in plants.

Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations

The present study reports profiling of the elevated carbon dioxide (CO2) concentration responsive global transcriptome in chickpea, along with a combinatorial approach for exploring interlinks between physiological and transcriptional changes, important for the climate change scenario. Various physiological parameters were recorded in two chickpea cultivars (JG 11 and KAK 2) grown in open top chambers under ambient [380 parts per million (ppm)] and two stressed/elevated CO2 concentrations (550 and 700 ppm), at different stages of plant growth. The elevated CO2 concentrations altered shoot and root length, nodulation (number of nodules), total chlorophyll content and nitrogen balance index, significantly. RNA-Seq from 12 tissues representing vegetative and reproductive growth stages of both cultivars under ambient and elevated CO2 concentrations identified 18,644 differentially expressed genes including 9,687 transcription factors (TF). The differential regulations in genes, gene networks and quantitative real-time polymerase chain reaction (qRT-PCR) -derived expression dynamics of stress-responsive TFs were observed in both cultivars studied. A total of 138 pathways, mainly involved in sugar/starch metabolism, chlorophyll and secondary metabolites biosynthesis, deciphered the crosstalk operating behind the responses of chickpea to elevated CO2 concentration.

An integrated research framework combining genomics, systems biology, physiology, modelling and breeding for legume improvement in response to elevated CO2 under climate change scenario

How unprecedented changes in climatic conditions will impact yield and productivity of some crops and their response to existing stresses, abiotic and biotic interactions is a key global concern. Climate change can also alter natural species' abundance and distribution or favor invasive species, which in turn can modify ecosystem dynamics and the provisioning of ecosystem services. Basic anatomical differences in C3 and C4 plants lead to their varied responses to climate variations. In plants having a C3 pathway of photosynthesis, increased atmospheric carbon dioxide (CO2) positively regulates photosynthetic carbon (C) assimilation and depresses photorespiration. Legumes being C3 plants, they may be in a favorable position to increase biomass and yield through various strategies. This paper comprehensively presents recent progress made in the physiological and molecular attributes in plants with special emphasis on legumes under elevated CO2 conditions in a climate change scenario. A strategic research framework for future action integrating genomics, systems biology, physiology and crop modelling approaches to cope with changing climate is also discussed. Advances in sequencing and phenotyping methodologies make it possible to use vast genetic and genomic resources by deploying high resolution phenotyping coupled with high throughput multi-omics approaches for trait improvement. Integrated crop modelling studies focusing on farming systems design and management, prediction of climate impacts and disease forecasting may also help in planning adaptation. Hence, an integrated research framework combining genomics, plant molecular physiology, crop breeding, systems biology and integrated crop-soil-climate modelling will be very effective to cope with climate change.

Silicon Compensates Phosphorus Deficit-Induced Growth Inhibition by Improving Photosynthetic Capacity, Antioxidant Potential, and Nutrient Homeostasis in Tomato

Phosphorus (P) deficiency in soils is a major problem for sustainable crop production worldwide. Silicon (Si) is a beneficial element that can promote plant growth, development and responses to stresses. However, the effect of Si on tomato (Solanum lycopersicum L.) growth, photosynthesis and mineral uptake under P deficit conditions and underlying mechanisms remain unclear. Here, we showed that low P (LP) supply inhibited tomato growth as revealed by significantly decreased fresh and dry weights of shoots and impaired root morphological traits. LP-induced growth inhibition was associated with decreased photosynthetic pigment content, net photosynthetic rate (Pn), stomatal conductance, transpiration rate and water use efficiency. However, exogenous Si application alleviated LP-induced decreases in growth and physiological parameters. In particular, Si increased Pn by 65.2%, leading to a significantly increased biomass accumulation. Biochemical quantification and in situ visualization of reactive oxygen species (ROS) showed increased ROS (O2−· and H2O2) accumulation under LP stress, which eventually elevated lipid peroxidation. Interestingly, exogenous Si decreased ROS and malondialdehyde levels by substantially increasing the activity of antioxidant enzymes, including superoxide dismutase, peroxidase, and catalase. In addition, Si increased concentrations of osmoregulatory substances, such as proline, soluble sugar, soluble proteins, free amino acids, and organic acids under LP stress. Analysis of major element concentrations revealed that exogenous Si application under LP stress not only increased Si uptake but also enhanced the concentrations of most essential elements (K, Na, Ca, Mg, Fe, and Mn) in different tissues (roots, leaves, and stems). These results reveal that Si mitigates LP stress by improving photosynthetic capacity, antioxidant potential, and nutrient homeostasis and that it can be used for agronomic management of vegetable crops in P-deficient soils.

Impact of Elevated CO2 on Seed Quality of Soybean at the Fresh Edible and Mature Stages

Although the effect of elevated CO2 (eCO2) on soybean yield has been well documented, few studies have addressed seed quality, particularly at the fresh edible (R6) and mature stages (R8). Under the current global scenario of increasing CO2 levels, this potentially threatens the nutritional content and quality of food crops. Using four soybean cultivars, we assessed the effects of eCO2 on the concentrations of crude protein, crude oil, and isoflavones and analyzed the changes in free amino acids, fatty acids, and mineral elements in seeds. At R6, eCO2 had no influence on soybean seed protein and oil concentrations. At R8, eCO2 significantly decreased seed protein concentration but increased seed oil concentration; it also significantly decreased total free amino acid concentration. However, at the same stage, the proportion of oleic acid (18:1) among fatty acids increased in response to eCO2 in the cultivars of Zhongke-maodou 2 (ZK-2) and Zhongke-maodou 3 (ZK-3), and a similar trend was found for linoleic acid (18:2) in Zhongke-maodou 1 (ZK-1) and Hei-maodou (HD). Total isoflavone concentrations increased significantly at both the R6 and R8 stages in response to eCO2. Compared with ambient CO2, the concentrations of K, Ca, Mg, P, and S increased significantly under eCO2 at R6, while the Fe concentration decreased significantly. The response of Zn and Mn concentrations to eCO2 varied among cultivars. At R8 and under eCO2, Mg, S, and Ca concentrations increased significantly, while Zn and Fe concentrations decreased significantly. These findings suggest that eCO2 is likely to benefit from the accumulation of seed fat and isoflavone but not from that of protein. In this study, the response of seed mineral nutrients to eCO2 varied between cultivars.

Differential response of hexaploid and tetraploid wheat to interactive effects of elevated [CO2] and low phosphorus

Hexaploid wheat is more responsive than tetraploid to the interactive effects of elevated [CO₂] and low P in terms of carboxylate efflux, enzyme activity and gene expression (TaPT1 and TaPAP). Availability of mineral nutrients to plants under changing climate has become a serious challenge to food security and economic development. An understanding of how elevated [CO₂] influences phosphorus (P) acquisition processes at the whole-plant level would be critical in selecting cultivars as well as to maintain optimum yield in limited-P conditions. Wheat (Triticum aestivum and T. durum) grown hydroponically with sufficient and low P concentration were exposed to elevated and ambient [CO₂]. Improved dry matter partitioning towards root resulted in increased root-to-shoot ratio, root length, volume, surface area, root hair length and density at elevated [CO₂] with low P. Interaction of low P and [CO₂] induced activity of enzymes (phosphoenolpyruvate carboxylase, malate dehydrogenase and citrate synthase) in root tissue resulting in twofold increase in carboxylates and acid phosphatase exudation. Physiological absorption capacity of roots showed that plants alter their uptake kinetics by increasing affinity (low K_m) in response to elevated [CO₂] under low P supply. Increased relative expression of genes, purple acid phosphatase (TaPAP) and high-affinity Pi transporter (TaPT1) in roots induced by elevated [CO₂] and low P supported our physiological observations. Hexaploid wheat (PBW-396) being more responsive to elevated [CO₂] at low P supply as compared to tetraploid (PDW-233) necessitates the ploidy effect to be explored further which might be advantageous under changing climate.

Molecular insights into photosynthesis and carbohydrate metabolism in Jatropha curcas grown under elevated CO2 using transcriptome sequencing and assembly

Jatropha curcas L. (Family - Euphorbiaceae) is a perennial tree of special interest due to its potential as a biofuel plant with high carbon sequestration. In this study, physiological investigations coupled with transcriptomics in relation to photosynthesis were evaluated in Jatropha grown under ambient (395 ppm) and elevated (550 ppm) CO2 atmosphere. Morphophysiological analysis revealed that Jatropha sustained enhanced photosynthesis during its growth under elevated CO2 for one year which might be linked to improved CO2 assimilation physiology and enhanced sink activity. We sequenced and analyzed the leaf transcriptome of Jatropha after one year of growth in both conditions using Illumina HiSeq platform. After optimized assembly, a total of 69,581 unigenes were generated. The differential gene expression (DGE) analysis revealed 3013 transcripts differentially regulated in elevated CO2 conditions. The photosynthesis regulatory genes were analysed for temporal expression patterns at four different growth phases which highlighted probable events contributing to enhanced growth and photosynthetic capacity including increased reducing power, starch synthesis and sucrose mobilization under elevated CO2. Overall, our data on physiological and transcriptomic analyses suggest an optimal resource allocation to the available and developing sink organs thereby sustaining improved photosynthetic rates during long-term growth of Jatropha under CO2 enriched environment.

Elevated CO2 levels modify TiO2 nanoparticle effects on rice and soil microbial communities

Evidence suggests that CO₂ modifies the behavior of nanomaterials. Thus, in a few decades, plants might be exposed to additional stress if atmospheric levels of CO₂ and the environmental burden of nanomaterials increase at the current pace. Here, we used a full-size free-air CO₂ enrichment (FACE) system in farm fields to investigate the effect of elevated CO₂ levels on phytotoxicity and microbial toxicity of nTiO₂ (0, 50, and 200mgkg^-1) in a paddy soil system. Results show that nTiO₂ did not induce visible signs of toxicity in rice plants cultivated at the ambient CO₂ level (370μmolmol^-1), but under the high CO₂ concentration (570μmolmol^-1) nTiO₂ significantly reduced rice biomass by 17.9% and 22.1% at 50mgkg^-1 and 200mgkg^-1, respectively, and grain yield by 20.8% and 44.1% at 50mgkg^-1 and 200mgkg^-1, respectively. In addition, at the high CO₂ concentration, nTiO₂ at 200mgkg^-1 increased accumulation of Ca, Mg, Mn, P, Zn, and Ti by 22.5%, 16.8%, 29.1%, 7.4%, 15.7% and 8.6%, respectively, but reduced fat and total sugar by 11.2% and 25.5%, respectively, in grains. Such conditions also changed the functional composition of soil microbial communities, alerting specific phyla of bacteria and the diversity and richness of protista. Overall, this study suggests that increases in CO₂ levels would modify the effects of nTiO₂ on the nutritional quality of crops and function of soil microbial communities, with unknown implications for future economics and human health.

High CO2 Primes Plant Biotic Stress Defences through Redox-Linked Pathways

Industrial activities have caused tropospheric CO₂ concentrations to increase over the last two centuries, a trend that is predicted to continue for at least the next several decades. Here, we report that growth of plants in a CO₂-enriched environment activates responses that are central to defense against pathogenic attack. Salicylic acid accumulation was triggered by high-growth CO₂ in Arabidopsis (Arabidopsis thaliana) and other plants such as bean (Phaseolus vulgaris). A detailed analysis in Arabidopsis revealed that elevated CO₂ primes multiple defense pathways, leading to increased resistance to bacterial and fungal challenge. Analysis of gene-specific mutants provided no evidence that activation of plant defense pathways by high CO₂ was caused by stomatal closure. Rather, the activation is partly linked to metabolic effects involving redox signaling. In support of this, genetic modification of redox components (glutathione contents and NADPH-generating enzymes) prevents full priming of the salicylic acid pathway and associated resistance by high CO₂ The data point to a particularly influential role for the nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase, a cytosolic enzyme whose role in plants remains unclear. Our observations add new information on relationships between high CO₂ and oxidative signaling and provide novel insight into plant stress responses in conditions of increased CO₂.