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Abstract Aquatic biota are threatened by climate warming as well as other anthropogenic stressors such as eutrophication by phosphates and nitrate. However, it remains unclear how nitrate exposure can alter the resilience of microalgae to climate warming, particularly heatwaves. To get a better understanding of these processes, we investigated the effect of elevated temperature and nitrate pollution on growth, metabolites (sugar and protein), oxidative damage (lipid peroxidation), and antioxidant accumulation (polyphenols, proline) in Chlamydomonas reinhardtii and Pseudokirchneriella subcapitata. The experiment involved a 3 × 3 factorial design, where microalgae were exposed to one of three nitrate levels (5, 50, or 200 mg L−1 NO3 −l) at 20 °C for 2 weeks. Subsequently, two heatwave scenarios were imposed: a short and moderate heatwave at 24 °C for 2 weeks, and a long and intense heatwave with an additional 2 weeks at 26 °C. A positive synergistic effect of heatwaves and nitrate on growth and metabolites was observed, but this also led to increased oxidative stress. In the short and moderate heatwave, oxidative damage was controlled by increased antioxidant levels. The high growth, metabolites, and antioxidants combined with low oxidative stress during the short and moderate heatwaves in moderate nitrate (50 mg L−1) led to a sustainable increased food availability to grazers. On the other hand, long and intense heatwaves in high nitrate conditions caused unsustainable growth due to increased oxidative stress and relatively low antioxidant (proline) levels, increasing the risk for massive algal die-offs.

Rice is a highly valuable crop consumed all over the world. Soil pollution, more specifically chromium (Cr), decreases rice yield and quality. Future climate CO2 (eCO2) is known to affect the growth and yield of crops as well as the quality parameters associated with human health. However, the detailed physiological and biochemical responses induced by Cr in rice grains produced under eCO2 have not been deeply studied. Cr (200 and 400 mg Cr6+/Kg soil) inhibited rice yield and photosynthesis in Sakha 106, but to less extend in Giza 181 rice cultivar. Elevated CO2 reduced Cr accumulation and, consequently, recovered the negative impact of the higher Cr dose, mainly in Sakha 106. This could be explained by improved photosynthesis which was consistent with increased carbohydrate level and metabolism (starch synthases and amylase). Moreover, these increases provided a route for the biosynthesis of organic, amino and fatty acids. At grain quality level, eCO2 differentially mitigated Cr stress-induced reductions in minerals (e.g., P, Mg and Ca), proteins (prolamin, globulin, albumin, glutelin), unsaturated fatty acids (e.g., C20:2 and C24:1) and antioxidants (phenolics and total antioxidant capacity) in both cultivars. This study provided insights into the physiological and biochemical bases of eCO2-induced grain yield and quality of Cr-stressed rice.

Abscisic acid (ABA) plays a vital role in the induction of low temperature tolerance in plants. To understand the molecular basis of this phenomenon, we performed a proteomic analysis on an ABA-deficit mutant barley (Az34) and its wild type (cv Steptoe) under control conditions (25/18 °C) and after exposure to 0 °C for 24 h. Most of the differentially abundant proteins were involved in the processes of photosynthesis and metabolisms of starch, sucrose, carbon, and glutathione. The chloroplasts in Az34 leaves were more severely damaged, and the decrease in Fv/Fm was larger in Az34 plants compared with WT under low temperature. Under low temperature, Az34 plants possessed significantly higher activities of ADP-glucose pyrophosphorylase, fructokinase, monodehydroascorbate reductase, and three invertases, but lower UDP-glucose pyrophosphorylase activity than WT. In addition, concentrations of proline and soluble protein were lower, while concentration of H2O2 was higher in Az34 plants compared to WT under low temperature. Collectively, the results indicated that ABA deficiency induced modifications in starch and sucrose biosynthesis and sucrolytic pathway and overaccumulation of reactive oxygen species were the main reason for depressed low temperature tolerance in barley, which provide novel insights to the response of barley to low temperature under future climate change.

Plants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here, we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signaling and clock mutants and identify a core set of photoperiod stress-responsive genes. Photoperiod stress caused altered expression of numerous reactive oxygen species (ROS)-related genes. Photoperiod stress-sensitive mutants displayed similar, but stronger transcriptomic changes than wild-type plants. The alterations showed a strong overlap with those occurring in response to ozone stress, pathogen attack and flagellin peptide (flg22)-induced PAMP triggered immunity (PTI), which have in common the induction of an apoplastic oxidative burst. Interestingly, photoperiod stress triggers transcriptional changes in jasmonic acid (JA) and salicylic acid (SA) biosynthesis and signaling and results in increased JA, SA and camalexin levels. These responses are typically observed after pathogen infections. Consequently, photoperiod stress increased the resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae pv. tomato DC3000. In summary, we show that photoperiod stress causes transcriptional reprogramming resembling plant pathogen defense responses and induces systemic acquired resistance (SAR) in the absence of a pathogen.

Drought negatively affects crop growth and development, so it is crucial to develop practical ways to reduce these consequences of water scarcity. The effect of the interactive potential of compost (Comp), mycorrhizal fungi (AMF), and carbon nanoparticles (CNPS) on plant growth, photosynthesis rate, primary metabolism, and secondary metabolism was studied as a novel approach to mitigating drought stress in maize plants. Drought stress significantly reduced maize growth and photosynthesis and altered metabolism. Here, the combined treatments Com-AMF or Com-AMF-CNPs mitigated drought-induced reductions in fresh and dry weights. The treatments with AMF or CNPS significantly increased photosynthesis (by 10%) in comparison to the control plants. Results show that soluble sugars were accumulated to maintain the osmotic status of the maize plant under drought stress. The level and metabolism of sucrose, an osmo-protectant, were increased in plants treated with Com (by 30%), which was further increased under the triple effect of Com-AMF-CNPs (40%), compared to untreated plants. This was inconsistent with increased sucrose-phosphate synthase and sucrose-P-synthase activity. The combined treatment Com-AMF-CNPs increased the levels of oxalic and succinic acids (by 100%) and has been reflected in the enhanced levels of amino acids such as the antioxidant and omso-protectant proline. Higher increases in fatty acids by treatment with CNPS were also recorded. Com-AMF-CNPs enhanced many of the detected fatty acids such as myristic, palmitic, arachidic, docosanoic, and pentacosanoic (110%, 30%, 100%, and 130%, respectively), compared to untreated plants. At the secondary metabolism level, sugar and amino acids provide a route for polyamine biosynthesis, where Com-AMF-CNPs increased spermine and spermidine synthases, ornithine decarboxylase, and adenosyl methionine decarboxylase in treated maize. Overall, our research revealed for the first time how Cmo, AMF, and/or CNPS alleviated drought stress in maize plants.

Seaweeds are well known for having a wealth of nutritional benefits and providing ecological support to associated fauna. Seasonality influences the biochemical characteristics, affecting their ecological and economic values. In the present study, we evaluated pigments, primary and secondary metabolites, minerals, and antioxidant properties of green seaweed Chaetomorpha antennina growing on the intertidal rocks along the Covelong coast, India, in different seasons (from June 2019 to March 2020). Significant variations were found in the levels of antioxidants, minerals, and metabolites in different seasons, e.g., amino acid levels were the highest in post-monsoon and the lowest in summer. In monsoon, we found the highest concentration of fatty acids in the thalli. Lipid peroxidation and total antioxidant activity were at their maximum levels during post-monsoon, which indicated oxidative damage responses. No significant variations were found in the levels of photosynthetic pigments. The outcomes indeed suggested seasonal variations in the biochemical and nutrient profile of C. antennina. We suggest that the harvesting/collection of C. antennina for different nutrients and metabolites should be performed in the respective seasons.

Ocimum basilicum is a valuable source of bioactive metabolites with high preventive and therapeutic effectiveness. Here we aimed to investigate the effect of phenological stages (vegetative and flowering stages) on essential oil composition and biological activities of two varieties of O. basilicum (Fino Verde variety and Genovese varieties). To this end, the level of essential oils, flavonoids and phenols, as well as antioxidant and antifungal activities were measured. At the metabolic level, essential oil at vegetative stage of O. bailicum Fino Verde and Genovese variety was constituted by 22 and 26 compounds representing 71.68% and 82.54% of the total oil, respectively. Where germacrene D (10.07%), bicyclogermacrene (6.07%) and β-elemene (4.88%) were the most present components in Fino Verde variety. Moreover, 22.19% are oxygenated monoterpenes represented mainly by the linalool (15.18%) and 1.8 cineole (6.36%) in Genovese variety. The individuals of essential oils were significantly increased to 40 components in Fino Verde variety (98.01% of total essential oil) and decreased to 15 components (95.6% of total essential oil) in Genovese variety at flowering stage. At this stage, the oxygenated monoterpenes (78.4%) were the major fraction represented by linalool (40.1%) and 1.8 cineole (30.96%) in Fino Verde variety, however 64.69% were esters which mainly represented by the methyl cinnamate (64.69%), and 16.83% of oxygenated monoterpenes and Linalool (12.7%) were recorded for Genovese variety. Genovese variety showed the highest levels at both vegetative and flowering stage compared to Fino Verde variety. At flowering stage, the two varieties showed high antioxidant and antifungal activities. Overall, O. basilicum properties offer prospects for their use as a source, particularly at flowering stage to extend new medicines based on natural bioactive molecules.

This study aims at exploiting salinity stress as an innovative, simple, and cheap method to enhance the production of antioxidant metabolites and enzymes from bacteria for potential application as functional additives to foods and pharmaceuticals. We investigated the physiological and biochemical responses of four bacterial isolates, which exhibited high tolerance to 20% NaCl (wt/vol), out of 27 bacterial strains isolated from Aushazia Lake, Qassim region, Saudi Arabia. The phylogenetic analysis of the 16S rRNA genes of these four isolates indicated that strains ST1 and ST2 belong to genus Bacillus, whereas strains ST3 and ST4 belong to genus Planococcus. Salinity stress differentially induced oxidative damage, where strains ST3 and ST4 showed increased lipid peroxidation, lipoxygenase, and xanthine oxidase levels. Consequently, high antioxidant contents were produced to control oxidative stress, particularly in ST3 and ST4. These two Planococcus strains showed increased glutathione cycle, phenols, flavonoids, antioxidant capacity, catalase, and/or superoxide dismutase (SOD). Interestingly, the production of glutathione by Planococcus strains was some thousand folds greater than by higher plants. On the other hand, the induction of antioxidants in ST1 and ST2 was restricted to phenols, flavonoids, peroxidase, glutaredoxin, and/or SOD. The hierarchical analysis also supported strain-specific responses. This is the first report that exploited salinity stress for promoting the production of antioxidants from bacterial isolates, which can be utilized as postbiotics for promising applications in foods and pharmaceuticals.

Although plant organ shapes are defined by spatio-temporal variations of directional tissue expansion, this is a little characterized aspect of organ growth regulation. Although it is well known that the plant hormone gibberellin increases the leaf length/with ratio, its effects on cell expansion in the growing leaf are largely unknown. To understand how variations in rate and anisotropy of growth establish the typical monocotelydonous leaf shape, we studied the leaf growth zone of maize (Zea mays) with a kinematic analysis of cell expansion in the three directions of growth: proximo-distal, medio-lateral, and dorso-ventral. To determine the effect of gibberellin, we compared a gibberellin-deficient dwarf3 mutant and the overproducing UBI::GA20OX-1 line with their wild types. We found that, as expected, longitudinal growth was dominant throughout the growth zone. The highest degree of anisotropy occurred in the division zone, where relative growth rates in width and thickness were almost zero. Growth anisotropy was smaller in the elongation zone, due to higher lateral and dorso-ventral growth rates. Growth in all directions stopped at the same position. Gibberellin increased the size of the growth zone and the degree of growth anisotropy by stimulating longitudinal growth rates. Inversely, the duration of expansion was negatively affected, so that mature cell length was unaffected, while width and height of cells were reduced. Our study provides a detailed insight in the dynamics of growth anisotropy in the maize leaf and demonstrates that gibberellin specifically stimulates longitudinal growth rates throughout the growth zone.

Marrubium vulgare is a valuable source of natural bioactive molecules with high preventive and therapeutic effectiveness. Therefore, this study aimed to study the chemical polymorphism of natural populations of M. vulgare in Tunisia by quantitative chemical markers and the estimation of divergence between populations. Phytochemical analyses of the eight natural populations of Tunisian Marrubium vulgare prospected in different bioclimatic stages, revealed 42 compounds of essential oils representing 96.08% to 100% of the total oil. Hydrocarbon sesquiterpenes were the main fraction of all the populations studied and β-bisabolene was the major compound (from 30.11% to 71.35% of the total oil). The phytochemical investigation of the M. vulgare plant indicated the presence of essential oil with significant percentages of phenolic compounds. A significant quantitative and qualitative variation in the essential oils is detected for both major and minor compounds. The principal components analysis (PCA) performed in the single and combined traits provides a good distinction among populations, not according to their geographical and/or bioclimatic origins. Moreover, the phytochemical analysis of the leaves showed that the Tunisian populations, i.e., the populations of Kasserine, Kef, and Beja, were very rich in phenolic compounds (from 20.8 to 44.65 mg GAE/g DW). Flavonoids compounds were also the main class of total polyphenols present in all the tested populations (from 8.91 to 37.48 mg RE/g DW). The quantitative genetic diversity estimated by the population’s structure, based on PCA analysis, was an adaptation to the changes in the environmental conditions. Overall, our study indicated that natural populations of M. vulgare had different chemotypes of essential oils and they were rich in phenolic compounds, particularly flavonoids, which opens a new prospect for industrial use and differential exploitation of this species.

Under normal and stress conditions plant growth require a complex interplay between phytohormones and reactive oxygen species (ROS). However, details of the nature of this crosstalk remain elusive. Here, we demonstrate that PINOID (PID), a serine threonine kinase of the AGC kinase family, perturbs auxin homeostasis, which in turn modulates rosette growth and induces stress responses in Arabidopsis plants. Arabidopsis mutants and transgenic plants with altered PID expression were used to study the effect on auxin levels and stress-related responses. In the leaves of plants with ectopic PID expression an accumulation of auxin, oxidative burst and disruption of hormonal balance was apparent. Furthermore, PID overexpression led to the accumulation of antioxidant metabolites, while pid knockout mutants showed only moderate changes in stress-related metabolites. These physiological changes in the plants overexpressing PID modulated their response toward external drought and osmotic stress treatments when compared to the wild type. Based on the morphological, transcriptome, and metabolite results, we propose that perturbations in the auxin hormone levels caused by PID overexpression, along with other hormones and ROS downstream, cause antioxidant accumulation and modify growth and stress responses in Arabidopsis. Our data provide further proof for a strong correlation between auxin and stress biology.

In plants many developmental processes are regulated by auxin and its directional transport. PINOID (PID) kinase helps to regulate this transport by influencing polar recruitment of PIN efflux proteins on the cellular membranes. We investigated how altered auxin levels affect leaf growth in Arabidopsis thaliana. Arabidopsis mutants and transgenic plants with altered PID expression levels were used to study the effect on auxin distribution and leaf development. Single knockouts showed small pleiotropic growth defects. Contrastingly, several leaf phenotypes related to changes in auxin concentrations and transcriptional activity were observed in PID overexpression (PIDOE) lines. Unlike in the knockout lines, the leaves of PIDOE lines showed an elevation in total indole-3-acetic acid (IAA). Accordingly, enhanced DR5-visualized auxin responses were detected, especially along the leaf margins. Kinematic analysis revealed that ectopic expression of PID negatively affects cell proliferation and expansion rates, yielding reduced cell numbers and small-sized cells in the PIDOE leaves. We used PIDOE lines as a tool to study auxin dose effects on leaf development and demonstrate that auxin, above a certain threshold, has a negative affect on leaf growth. RNA sequencing further showed how subtle PIDOE-related changes in auxin levels lead to transcriptional reprogramming of cellular processes.

Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time.Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems.Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.

Studies regarding macroalgal responses to ocean acidification (OA) are mostly limited to short-term experiments in controlled conditions, which hamper the possibility to scale up the observations to long-term effects in the natural environment. To gain a broader perspective, we utilized volcanic CO2 vents as a “natural laboratory” to study OA effects on Sargassum vulgare at different time scales. We measured photosynthetic rates, oxidative stress levels, antioxidant contents, antioxidant enzyme activities, and activities of oxidative metabolic enzymes in S. vulgare growing at a natural acidified site (pH 6.7) compared to samples from a site with current pH (pH 8.2), used as a control one. These variables were also tested in plants transplanted from the control to the acidified site and vice-versa. After short-term exposure, photosynthetic rates and energy metabolism were increased in S. vulgare together with oxidative damage. However, in natural populations under long-term conditions photosynthetic rates were similar, the activity of oxidative metabolic enzymes was maintained, and no sign of oxidative damages was observed. The differences in the response of the macroalga indicate that the natural population at the acidified site is adapted to live at the lowered pH. The results suggest that this macroalga can adopt biochemical and physiological strategies to grow in future acidified oceans.

Motivation: Genome-scale ‘omics’ data constitute a potentially rich source of information about biological systems and their function. There is a plethora of tools and methods available to mine omics data. However, the diversity and complexity of different omics data types is a stumbling block for multi-data integration, hence there is a dire need for additional methods to exploit potential synergy from integrated orthogonal data. Rough Sets provide an efficient means to use complex information in classification approaches. Here, we set out to explore the possibilities of Rough Sets to incorporate diverse information sources in a functional classification of unknown genes. Results: We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features and Gene Ontology (GO) annotations were combined to describe general and biologically relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms); whereas, models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations. Finally, we studied cell cycle protein–protein interactions derived from both tandem affinity purification experiments and in silico experiments in the BioGRID interactome database and found strong experimental evidence for the predictions generated by our models. The results show that our approach can be used to build very robust models that create synergy from integrating gene expression data and protein features. Availability: The Rough Set-based method is implemented in the Rosetta toolkit kernel version 1.0.1 available at: http://rosetta.lcb.uu.se/ Contact: kuiper@nt.ntnu.no; krwab@psb.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

In recent years there has been a strong development of computational approaches to mechanistically understand organ growth regulation in plants. In this study, simulation methods were used to explore which regulatory mechanisms can lead to realistic output at the cell and whole organ scale and which other possibilities must be discarded as they result in cellular patterns and kinematic characteristics that are not consistent with experimental observations for the Arabidopsis thaliana primary root. To aid in this analysis, a 'Uniform Longitudinal Strain Rule' (ULSR) was formulated as a necessary condition for stable, unidirectional, symplastic growth. Our simulations indicate that symplastic structures are robust to differences in longitudinal strain rates along the growth axis only if these differences are small and short-lived. Whereas simple cell-autonomous regulatory rules based on counters and timers can produce stable growth, it was found that steady developmental zones and smooth transitions in cell lengths are not feasible. By introducing spatial cues into growth regulation, those inadequacies could be avoided and experimental data could be faithfully reproduced. Nevertheless, a root growth model based on previous polar auxin-transport mechanisms violates the proposed ULSR due to the presence of lateral gradients. Models with layer-specific regulation or layer-driven growth offer potential solutions. Alternatively, a model representing the known cross-talk between auxin, as the cell proliferation promoting factor, and cytokinin, as the cell differentiation promoting factor, predicts the effect of hormone-perturbations on meristem size. By down-regulating PIN-mediated transport through the transcription factor SHY2, cytokinin effectively flattens the lateral auxin gradient, at the basal boundary of the division zone, (thereby imposing the ULSR) to signal the exit of proliferation and start of elongation. This model exploration underlines the value of generating virtual root growth kinematics to dissect and understand the mechanisms controlling this biological system.